Mercurial > repos > devteam > fastx_reverse_complement
changeset 2:43540312cb76 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:41:59 -0400 |
| parents | a710c1b9776b |
| children | 9d06c848a628 |
| files | fastx_reverse_complement.xml tool_dependencies.xml |
| diffstat | 2 files changed, 29 insertions(+), 31 deletions(-) [+] |
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--- a/fastx_reverse_complement.xml Tue Nov 26 12:49:47 2013 -0500 +++ b/fastx_reverse_complement.xml Tue Oct 13 12:41:59 2015 -0400 @@ -1,41 +1,40 @@ <tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement"> - <description></description> + <description></description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command>zcat -f '$input' | fastx_reverse_complement -v -o $output + <command> +<![CDATA[ +zcat -f < '$input' | fastx_reverse_complement -v -o '$output' #if $input.ext == "fastqsanger": --Q 33 + -Q 33 #end if - </command> - <inputs> - <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" /> - </inputs> - - <tests> - <test> - <!-- Reverse-complement a FASTA file --> - <param name="input" value="fastx_rev_comp1.fasta" /> - <output name="output" file="fastx_reverse_complement1.out" /> - </test> - <test> - <!-- Reverse-complement a FASTQ file --> - <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/> - <output name="output" file="fastx_reverse_complement2.out" /> - </test> - </tests> - - - <outputs> - <data format="input" name="output" metadata_source="input" /> - </outputs> - -<help> +]]> + </command> + <inputs> + <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" /> + </inputs> + <outputs> + <data format_source="input" name="output" metadata_source="input" /> + </outputs> + <tests> + <test> + <!-- Reverse-complement a FASTA file --> + <param name="input" value="fastx_rev_comp1.fasta" /> + <output name="output" ftype="fasta" file="fastx_reverse_complement1.out" /> + </test> + <test> + <!-- Reverse-complement a FASTQ file --> + <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/> + <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" /> + </test> + </tests> + <help> **What it does** This tool reverse-complements each sequence in a library. If the library is a FASTQ, the quality-scores are also reversed. - + -------- **Example** @@ -60,6 +59,5 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - -</help> + </help> </tool>
--- a/tool_dependencies.xml Tue Nov 26 12:49:47 2013 -0500 +++ b/tool_dependencies.xml Tue Oct 13 12:41:59 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="fastx_toolkit" version="0.0.13"> - <repository changeset_revision="1cd326991d32" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e76e81b3eccf" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>