Mercurial > repos > devteam > fastx_artifacts_filter
changeset 2:09070cacefd8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:38:23 -0500 |
| parents | c8808979ba33 |
| children | dd3737e40dce |
| files | fastx_artifacts_filter.xml tool_dependencies.xml |
| diffstat | 2 files changed, 30 insertions(+), 30 deletions(-) [+] |
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--- a/fastx_artifacts_filter.xml Tue Dec 03 12:36:13 2013 -0500 +++ b/fastx_artifacts_filter.xml Wed Nov 11 12:38:23 2015 -0500 @@ -1,36 +1,36 @@ <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> - <description></description> - <requirements> + <description></description> + <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output" + <command> +<![CDATA[ +zcat -f < '$input' | fastx_artifacts_filter -v -o '$output' #if $input.ext == "fastqsanger": --Q 33 + -Q 33 #end if - </command> - - <inputs> - <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> - - </inputs> +]]> + </command> - <tests> - <test> - <!-- Filter FASTA file --> - <param name="input" value="fastx_artifacts1.fasta" /> - <param name="output" file="fastx_artifacts1.out" /> - </test> - <test> - <!-- Filter FASTQ file --> - <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> - <param name="output" file="fastx_artifacts2.out" /> - </test> - </tests> - - <outputs> - <data format="input" name="output" metadata_source="input" /> - </outputs> -<help> + <inputs> + <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> + </inputs> + <outputs> + <data format_source="input" name="output" metadata_source="input" /> + </outputs> + <tests> + <test> + <!-- Filter FASTA file --> + <param name="input" value="fastx_artifacts1.fasta" /> + <output name="output" ftype="fasta" file="fastx_artifacts1.out" /> + </test> + <test> + <!-- Filter FASTQ file --> + <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> + <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" /> + </test> + </tests> + <help> **What it does** This tool filters sequencing artifacts (reads with all but 3 identical bases). @@ -81,12 +81,12 @@ AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA - + ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ -</help> + </help> <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>
--- a/tool_dependencies.xml Tue Dec 03 12:36:13 2013 -0500 +++ b/tool_dependencies.xml Wed Nov 11 12:38:23 2015 -0500 @@ -1,6 +1,6 @@ <?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="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>