Mercurial > repos > devteam > fastq_to_fasta
diff fastq_to_fasta.xml @ 2:ce309f4ff17f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
| author | iuc |
|---|---|
| date | Tue, 08 May 2018 13:26:51 -0400 |
| parents | 186b8d913e6c |
| children | 02a5f43cd5d1 |
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--- a/fastq_to_fasta.xml Wed Nov 11 12:38:08 2015 -0500 +++ b/fastq_to_fasta.xml Tue May 08 13:26:51 2018 -0400 @@ -1,52 +1,54 @@ -<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.0"> - <description>converter</description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v -#if $input.ext == "fastqsanger": --Q 33 -#end if - </command> - - <inputs> - <param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" /> - - <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> - <option value="">yes</option> - <option value="-n">no</option> - </param> - - <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> - <option value="-r">yes</option> - <option value="">no</option> - </param> - - </inputs> - - <tests> - <test> - <!-- FASTQ-To-FASTA, keep N, don't rename --> - <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> - <param name="SKIPN" value=""/> - <param name="RENAMESEQ" value=""/> - <output name="output" file="fastq_to_fasta1a.out" /> - </test> - <test> - <!-- FASTQ-To-FASTA, discard N, rename --> - <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> - <param name="SKIPN" value="no"/> - <param name="RENAMESEQ" value="yes"/> - <output name="output" file="fastq_to_fasta1b.out" /> - </test> - </tests> - - <outputs> - <data format="fasta" name="output" metadata_source="input" /> - </outputs> - -<help> - +<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.1"> + <description>converter from FASTX-toolkit</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +@CATS@ fastq_to_fasta +$SKIPN +$RENAMESEQ +-o '$output' +-v @FQQUAL@ + ]]></command> + <inputs> + <expand macro="fastq_input" /> + <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> + <option value="">yes</option> + <option value="-n">no</option> + </param> + <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> + <option value="-r">yes</option> + <option value="">no</option> + </param> + </inputs> + <outputs> + <data name="output" format="fasta" metadata_source="input" /> + </outputs> + <tests> + <test> + <!-- FASTQ-To-FASTA, keep N, don't rename --> + <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> + <param name="SKIPN" value=""/> + <param name="RENAMESEQ" value=""/> + <output name="output" file="fastq_to_fasta1a.out" /> + </test> + <test> + <!-- FASTQ-To-FASTA, discard N, rename --> + <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> + <param name="SKIPN" value="no"/> + <param name="RENAMESEQ" value="yes"/> + <output name="output" file="fastq_to_fasta1b.out" /> + </test> + <test> + <!-- FASTQ-To-FASTA, discard N, rename --> + <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" /> + <param name="SKIPN" value="no"/> + <param name="RENAMESEQ" value="yes"/> + <output name="output" file="fastq_to_fasta-out2.out" /> + </test> + </tests> + <help><![CDATA[ **What it does** This tool converts data from Solexa format to FASTA format (scroll down for format description). @@ -77,6 +79,7 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ -</help> + ]]></help> + <expand macro="citations" /> <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>