| Next changeset 1:054c3355458d (2022-09-30) |
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Commit message:
planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0 |
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added:
seqcomplexity.xml test-data/example.fastq.gz test-data/example.fastq.notgzextension test-data/example.fastqsanger |
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| diff -r 000000000000 -r f14a21f3d5b1 seqcomplexity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqcomplexity.xml Tue Jun 07 09:29:15 2022 +0000 |
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| @@ -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> |
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| Binary file test-data/example.fastq.gz has changed |
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| Binary file test-data/example.fastq.notgzextension has changed |
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| diff -r 000000000000 -r f14a21f3d5b1 test-data/example.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.fastqsanger Tue Jun 07 09:29:15 2022 +0000 |
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| @@ -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 |