Mercurial > repos > devteam > fastx_collapser
changeset 2:17bfc147c9ea draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:41:05 -0400 |
| parents | 460c78dbadf8 |
| children | 7bda0f25191f |
| files | fastx_collapser.xml tool_dependencies.xml |
| diffstat | 2 files changed, 26 insertions(+), 26 deletions(-) [+] |
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--- a/fastx_collapser.xml Tue Nov 26 12:47:40 2013 -0500 +++ b/fastx_collapser.xml Tue Oct 13 12:41:05 2015 -0400 @@ -1,31 +1,32 @@ <tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse"> - <description>sequences</description> + <description>sequences</description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command>zcat -f '$input' | fastx_collapser -v -o '$output' + <command> +<![CDATA[ +zcat -f < '$input' | fastx_collapser -v -o '$output' #if $input.ext == "fastqsanger": --Q 33 + -Q 33 #end if - </command> - - <inputs> - <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" /> - </inputs> +]]> + </command> - <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines. - <tests> - <test> - <param name="input" value="fasta_collapser1.fasta" /> - <output name="output" file="fasta_collapser1.out" /> - </test> - </tests> + <inputs> + <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" /> + </inputs> + <outputs> + <data format="fasta" name="output" metadata_source="input" /> + </outputs> + <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines. + <tests> + <test> + <param name="input" value="fasta_collapser1.fasta" /> + <param name="output" file="fasta_collapser1.out" /> + </test> + </tests> --> - <outputs> - <data format="fasta" name="output" metadata_source="input" /> - </outputs> - <help> - + <help> **What it does** This tool collapses identical sequences in a FASTA file into a single sequence. @@ -34,7 +35,7 @@ **Example** -Example Input File (Sequence "ATAT" appears multiple times):: +Example Input File (Sequence "ATAT" appears multiple times):: >CSHL_2_FC0042AGLLOO_1_1_605_414 TGCG @@ -65,10 +66,10 @@ TGAG >5-1 TTCA - + .. class:: infomark -Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. +Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. @@ -85,6 +86,5 @@ 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 12:47:40 2013 -0500 +++ b/tool_dependencies.xml Tue Oct 13 12:41:05 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>