Mercurial > repos > devteam > fasta_nucleotide_changer
changeset 2:1cabf6626797 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:39:17 -0400 |
| parents | 8789a0450ad4 |
| children | ea1b0d77314d |
| files | fasta_nucleotide_changer.xml tool_dependencies.xml |
| diffstat | 2 files changed, 31 insertions(+), 34 deletions(-) [+] |
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--- a/fasta_nucleotide_changer.xml Tue Nov 26 12:43:28 2013 -0500 +++ b/fasta_nucleotide_changer.xml Tue Oct 13 12:39:17 2015 -0400 @@ -1,39 +1,37 @@ <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" > - <description>converter</description> + <description>converter</description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command>zcat -f '$input' | fasta_nucleotide_changer -$mode -v -o $output</command> - <inputs> - <param format="fasta" name="input" type="data" label="Library to convert" /> - - <param name="mode" type="select" label="Convert"> - <option value="d">RNA to DNA (U to T)</option> - <option value="r">DNA to RNA (T to U)</option> - </param> - </inputs> + <command> +<![CDATA[ +zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output' +]]> + </command> + <inputs> + <param format="fasta" name="input" type="data" label="Library to convert" /> - <!-- - Functional tests with param value starting with - fail. - --> - <tests> - <test> - <param name="input" value="fasta_nuc_changer1.fasta" /> - <param name="mode" value="r" /> - <output name="output" file="fasta_nuc_change1.out" /> - </test> - <test> - <param name="input" value="fasta_nuc_changer2.fasta" /> - <param name="mode" value="d" /> - <output name="output" file="fasta_nuc_change2.out" /> - </test> - </tests> - - <outputs> - <data format="input" name="output" metadata_source="input" /> - </outputs> - -<help> + <param name="mode" type="select" label="Convert"> + <option value="d">RNA to DNA (U to T)</option> + <option value="r">DNA to RNA (T to U)</option> + </param> + </inputs> + <outputs> + <data format_source="input" name="output" metadata_source="input" /> + </outputs> + <tests> + <test> + <param name="input" value="fasta_nuc_changer1.fasta" /> + <param name="mode" value="r" /> + <output name="output" ftype="fasta" file="fasta_nuc_change1.out" /> + </test> + <test> + <param name="input" value="fasta_nuc_changer2.fasta" /> + <param name="mode" value="d" /> + <output name="output" ftype="fasta" file="fasta_nuc_change2.out" /> + </test> + </tests> + <help> **What it does** This tool converts RNA FASTA files to DNA (and vice-versa). @@ -70,6 +68,5 @@ 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 12:43:28 2013 -0500 +++ b/tool_dependencies.xml Tue Oct 13 12:39:17 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>