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changeset 0:f14a21f3d5b1 draft

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planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0
author iuc
date Tue, 07 Jun 2022 09:29:15 +0000
parents
children 054c3355458d
files seqcomplexity.xml test-data/example.fastq.gz test-data/example.fastq.notgzextension test-data/example.fastqsanger
diffstat 4 files changed, 86 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqcomplexity.xml	Tue Jun 07 09:29:15 2022 +0000
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<tool id="seqcomplexity" name="Calculate sequence complexity" version="@TOOL_VERSION@" profile="21.05">
+  <description>total and per read</description>
+  <macros>
+    <token name="@TOOL_VERSION@">0.1.0</token>
+  </macros>
+  <requirements>
+    <requirement type="package" version="@TOOL_VERSION@">seqcomplexity</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+        seqcomplexity --fastq '$input_fastq' > '$output_json'
+    ]]></command>
+  <inputs>
+    <param name="input_fastq" type="data" format="fastq" label="Input reads in FASTQ format"/>
+  </inputs>
+  <outputs>
+    <data name="output_json" format="json"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_fastq" value="example.fastqsanger"/>
+      <output name="output_json">
+        <assert_contents>
+          <has_text_matching expression="complexity"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="input_fastq" value="example.fastq.gz"/>
+      <output name="output_json">
+        <assert_contents>
+          <has_text_matching expression="complexity"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="input_fastq" value="example.fastq.notgzextension"/>
+      <output name="output_json">
+        <assert_contents>
+          <has_text_matching expression="complexity"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+		Calculates Per-Read and Total Sequence Complexity from FastQ file. Complexity is the number of base pairs of unique or nonrepeating DNA in a given segment of DNA, or component of the genome. 
+	]]></help>
+  <citations>
+	</citations>
+</tool>
Binary file test-data/example.fastq.gz has changed
Binary file test-data/example.fastq.notgzextension has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fastqsanger	Tue Jun 07 09:29:15 2022 +0000
@@ -0,0 +1,36 @@
+@SRR17309642.1 1 length=76
+NCGAGGGGGCGGCCGCCTTTCCGGCCGCACCCCGTTTCCCAGGACGAAGGGCACTCCGCACCGGACCCCGGTCCCG
++SRR17309642.1 1 length=76
+#8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+@SRR17309642.2 2 length=76
+NTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAATACGAATGCCCCCGGCCGTCCCTCTTAATCAT
++SRR17309642.2 2 length=76
+#8BCCGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+@SRR17309642.3 3 length=76
+NACTTAATCAACGCAAGCTTATGACCCGCACTTACTGGGAATTCCTCGTTCATGGGGAATAATTGCAATCCCCGAT
++SRR17309642.3 3 length=76
+#8ACCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGD
+@SRR17309642.4 4 length=76
+NTTGACTCTAGTCTGGCACGGTGAAGAGACATGAGAGGTGTAGAATAAGTGGGAGGCCCCCGGCGCCCCCCCGTCC
++SRR17309642.4 4 length=76
+#8ACCFFFEFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEEGFGGGGGGGGGGGGGGGGGG
+@SRR17309642.5 5 length=76
+NTTCCACAAGAACAGCCTTAGCGAAAGGCTTCTTGAAGGGAAAGATGTAACTCTGTGAGATGAATTAACAGAACAC
++SRR17309642.5 5 length=76
+#8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC
+@SRR17309642.6 6 length=76
+NCCCTTCGTCCTGGGAAACGGGGTGCGGCCGGAAAGGCGGCCGCCCCCTCGCCCGTCACGCAACGCACGTTCGTGG
++SRR17309642.6 6 length=76
+#8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+@SRR17309642.7 7 length=75
+NTAAAACTACCCAATATGCTTTTTTTTTTTTTTTTCCCCAATATGCTTTTAAAGAAATATTTATGTTATGATAAA
++SRR17309642.7 7 length=75
+#8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGFGGGCEFEFGG
+@SRR17309642.8 8 length=76
+NCCGGGCCCGGGTCTTCCCGGAGTCGGGTTGCTTGGGAATGCAGCCCAAAGCGGGTGGTAAACTCCATCTAAGGCT
++SRR17309642.8 8 length=76
+#8ACCGGGGGGGGGGGFGGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGGGGGGF
+@SRR17309642.9 9 length=75
+NGGGGCTGCACGCGCGCTACACTGACTGGCTCAGCGTGTGCCTACCCTACGCCGGCAGGCGCGGGTAACCCGTTG
++SRR17309642.9 9 length=75
+#8BCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG