Mercurial > repos > devteam > fasta_clipping_histogram

changeset 2:9db07fd39f85 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:53:35 -0400
parents f666895cbebd
children 8889eb864cef
files fasta_clipping_histogram.xml macros.xml test-data/fasta_clipping_histogram-in1.fa test-data/fasta_clipping_histogram-in2.fa test-data/fasta_clipping_histogram-out1.png test-data/fasta_clipping_histogram-out2.png test-data/input.fasta tool_dependencies.xml
diffstat 8 files changed, 190 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/fasta_clipping_histogram.xml	Wed Nov 11 12:36:37 2015 -0500
+++ b/fasta_clipping_histogram.xml	Tue May 08 12:53:35 2018 -0400
@@ -1,20 +1,35 @@
-<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0">
+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.1">
     <description>chart</description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>fasta_clipping_histogram.pl $input $outfile</command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.49">perl-gdgraph</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+fasta_clipping_histogram.pl
+'$input'
+'$outfile'
+    ]]></command>
 
     <inputs>
-        <param format="fasta" name="input" type="data" label="Library to analyze" />
+        <expand macro="fasta_input" />
     </inputs>
 
     <outputs>
-        <data format="png" name="outfile" metadata_source="input" />
+        <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>
+    <help><![CDATA[
 **What it does**
 
 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
@@ -41,19 +56,19 @@
 
 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
+    >sequence1
+    AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+    >sequence2
+    GTGTGTGTGGGAAGTTGACACAGTA
+    >sequence3
+    CCTTGAGATTAACGCTAATCAAGTAAAC
 
 If the sequences span over multiple lines::
 
-   >sequence1
-   CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
-   TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
-   aactggtctttacctTTAAGTTG
+    >sequence1
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+    TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+    aactggtctttacctTTAAGTTG
 
 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
 
@@ -98,6 +113,7 @@
 
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
- .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+.. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue May 08 12:53:35 2018 -0400
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@CATS@">
+        #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+            zcat -f '$input' |
+        #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
+            bzcat -f '$input' |
+        #else:
+            cat '$input' |
+        #end if
+    </token>
+    <token name="@FQQUAL@">
+        <![CDATA[
+            #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
+                -Q 33
+            #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
+                -Q 64
+            #end if
+        ]]>
+    </token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <token name="@VERSION@">0.0.14</token>
+    <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
+    <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
+    <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
+    <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
+    <token name="@FASTAS@">fasta,fasta.gz</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{agordon,
+                    author = "Assaf Gordon",
+                    title = "FASTQ/A short-reads pre-processing tools",
+                    year = "2010",
+                    note = "http://hannonlab.cshl.edu/fastx_toolkit/",
+                    url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
+            </citation>
+        </citations>
+    </xml>
+    <xml name="fasta_input">
+        <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
+    </xml>
+    <xml name="fastq_input">
+        <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
+    </xml>
+    <xml name="fastx_input">
+        <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_clipping_histogram-in1.fa	Tue May 08 12:53:35 2018 -0400
@@ -0,0 +1,10 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_clipping_histogram-in2.fa	Tue May 08 12:53:35 2018 -0400
@@ -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
Binary file test-data/fasta_clipping_histogram-out1.png has changed
Binary file test-data/fasta_clipping_histogram-out2.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta	Tue May 08 12:53:35 2018 -0400
@@ -0,0 +1,6 @@
+>sequence1
+AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+>sequence2
+GTGTGTGTGGGAAGTTGACACAGTA
+>sequence3
+CCTTGAGATTAACGCTAATCAAGTAAAC
\ No newline at end of file
--- a/tool_dependencies.xml	Wed Nov 11 12:36:37 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="fastx_toolkit" version="0.0.13">
-        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>