Migrate fastx toolkit from tools-devteam, condafy.

.travis.yml

@@ -29,7 +29,7 @@ jobs:
       script:
         - set -e
         - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git,./deprecated/ .
-        - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list
+        - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list
 
     - stage: test
       env: CHUNK=0

tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml

@@ -0,0 +1,13 @@
+categories:
+- Fasta Manipulation
+- Graphics
+- Statistics
+description: Length Distribution chart
+long_description: |
+  This tool creates a histogram image of sequence lengths distribution
+  in a given fasta dataset file.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fasta_clipping_histogram
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram
+type: unrestricted

tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml

@@ -0,0 +1,119 @@
+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.1">
+    <description>chart</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.49">perl-gdgraph</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+fasta_clipping_histogram.pl
+'$input'
+'$outfile'
+    ]]></command>
+
+    <inputs>
+        <expand macro="fasta_input" />
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="png" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fasta_clipping_histogram-in1.fa" />
+            <output name="outfile" file="fasta_clipping_histogram-out1.png" compare="sim_size" delta="512" />
+        </test>
+        <test>
+            <param name="input" value="fasta_clipping_histogram-in2.fa" />
+            <output name="outfile" file="fasta_clipping_histogram-out2.png" compare="sim_size" delta="512" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
+
+**TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
+
+-----
+
+**Output Examples**
+
+In the following library, most sequences are 24-mers to 27-mers.
+This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png
+
+In the following library, most sequences are 19,22 or 23-mers.
+This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png
+
+-----
+
+**Input Formats**
+
+This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
+
+    >sequence1
+    AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+    >sequence2
+    GTGTGTGTGGGAAGTTGACACAGTA
+    >sequence3
+    CCTTGAGATTAACGCTAATCAAGTAAAC
+
+If the sequences span over multiple lines::
+
+    >sequence1
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+    TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+    aactggtctttacctTTAAGTTG
+
+Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
+
+   >sequence1
+   CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+-----
+
+**Multiplicity counts (a.k.a reads-count)**
+
+If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing).
+
+Example 1 - The following FASTA file *does not* have multiplicity counts::
+
+    >seq1
+    GGATCC
+    >seq2
+    GGTCATGGGTTTAAA
+    >seq3
+    GGGATATATCCCCACACACACACAC
+
+Each sequence is counts as one, to produce the following chart:
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png
+
+Example 2 - The following FASTA file have multiplicity counts::
+
+    >seq1-2
+    GGATCC
+    >seq2-10
+    GGTCATGGGTTTAAA
+    >seq3-3
+    GGGATATATCCCCACACACACACAC
+
+The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png
+
+Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+.. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>

tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml

@@ -0,0 +1 @@
+../macros.xml

tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa

@@ -0,0 +1,10 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA

tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in2.fa

@@ -0,0 +1,84 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA
+GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG
+TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA
+ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA
+CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT
+TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA
+AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT
+CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG
+CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC
+CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT
+TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC
+ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA
+AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC
+ATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGC
+TACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT
+ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGT
+TCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCA
+TAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTT
+TCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaat
+ttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaa
+tacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt
+gtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatag
+tgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaacct
+tgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttca
+caatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAA
+CACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT
+GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAG
+AAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTG
+AAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAA
+AACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAA
+ATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT
+CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATT
+TGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACG
+GTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAA
+ATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTAT
+CCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATA
+AACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCA
+TTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATG
+ATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATT
+GTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT
+ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATG
+ATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTG
+GTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTT
+GGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCT
+GCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt
+gataatttttttttctttgataatttttttctttttctttaataaattttttggataatt
+tttttttggataaatagttcttttttgataattctaataatttttttatttatttttttt
+ttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTA
+ACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAA
+GACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACA
+TTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtg
+tgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgt
+ACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA
+ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgt
+gagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCAT
+GAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGG
+AAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGA
+GAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA
+AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGC
+AGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaa
+aaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttcc
+ctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtc
+aaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTT
+TGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCT
+GTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttctt
+gtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAG
+TTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT
+TTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctct
+ttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTT
+GCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGT
+TGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATT
+ATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA
+GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTT
+AACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGC
+TTTGATGCCAATCCAACAATTTTGCATATATTA

tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/input.fasta

@@ -0,0 +1,6 @@
+>sequence1
+AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+>sequence2
+GTGTGTGTGGGAAGTTGACACAGTA
+>sequence3
+CCTTGAGATTAACGCTAATCAAGTAAAC

tool_collections/fastx_toolkit/fasta_formatter/.shed.yml

@@ -0,0 +1,10 @@
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+categories:
+- Fasta Manipulation
+description: FASTA Width formatter
+long_description: |
+  This tool re-formats a FASTA file, changing the width of the nucleotides lines.
+name: fasta_formatter
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter
+type: unrestricted

tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml

@@ -0,0 +1,91 @@
+<tool id="cshl_fasta_formatter" version="1.0.1" name="FASTA Width">
+    <description>formatter</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <!--
+        Note:
+            fasta_formatter also has a tabular output mode (-t),
+            but Galaxy already contains such a tool, so no need
+            to offer the user a duplicated tool.
+
+            So this XML tool only changes the width (line-wrapping) of a
+            FASTA file.
+    -->
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fasta_formatter
+-w $width
+-o '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="fasta_input" />
+
+        <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Re-format a FASTA file into a single line -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="0" />
+            <output name="output" file="fasta_formatter1.out" />
+        </test>
+        <test>
+            <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="60" />
+            <output name="output" file="fasta_formatter2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool re-formats a FASTA file, changing the width of the nucleotides lines.
+
+**TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
+
+--------
+
+**Example**
+
+Input FASTA file (each nucleotides line is 50 characters long)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
+    CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
+    TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
+    ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+    TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+    aactggtctttacctTTAAGTTG
+
+
+Output FASTA file (with width=80)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
+    ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
+    ATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
+    GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+Output FASTA file (with width=0 => single line)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>

tool_collections/fastx_toolkit/fasta_formatter/macros.xml

@@ -0,0 +1 @@
+../macros.xml