| Previous changeset 1:1dbb5181c327 (2013-12-03) Next changeset 3:859422bcb689 (2018-05-08) |
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Commit message:
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 |
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modified:
fasta_formatter.xml tool_dependencies.xml |
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| diff -r 1dbb5181c327 -r 9457a20156db fasta_formatter.xml --- a/fasta_formatter.xml Tue Dec 03 12:36:12 2013 -0500 +++ b/fasta_formatter.xml Mon Oct 12 10:15:31 2015 -0400 |
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| @@ -1,48 +1,49 @@ <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> - <description>formatter</description> + <description>formatter</description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <!-- - Note: - fasta_formatter also has a tabular output mode (-t), - but Galaxy already contains such a tool, so no need - to offer the user a duplicated tool. + <!-- + Note: + fasta_formatter also has a tabular output mode (-t), + but Galaxy already contains such a tool, so no need + to offer the user a duplicated tool. - So this XML tool only changes the width (line-wrapping) of a - FASTA file. - --> - <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command> - <inputs> - <param format="fasta" name="input" type="data" label="Library to re-format" /> - - <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> - </inputs> + So this XML tool only changes the width (line-wrapping) of a + FASTA file. + --> + <command> +<![CDATA[ +zcat -f < '$input' | fasta_formatter -w $width -o '$output' +]]> + </command> + <inputs> + <param format="fasta" name="input" type="data" label="Library to re-format" /> - <tests> - <test> - <!-- Re-format a FASTA file into a single line --> - <param name="input" value="fasta_formatter1.fasta" /> - <param name="width" value="0" /> - <param name="output" file="fasta_formatter1.out" /> - </test> - <test> - <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> - <param name="input" value="fasta_formatter1.fasta" /> - <param name="width" value="60" /> - <param name="output" file="fasta_formatter2.out" /> - </test> - </tests> - - <outputs> - <data format="input" name="output" metadata_source="input" /> - </outputs> - -<help> + <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> + </inputs> + <outputs> + <data format="fasta" name="output" metadata_source="input" /> + </outputs> + <tests> + <test> + <!-- Re-format a FASTA file into a single line --> + <param name="input" value="fasta_formatter1.fasta" /> + <param name="width" value="0" /> + <output name="output" file="fasta_formatter1.out" /> + </test> + <test> + <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes --> + <param name="input" value="fasta_formatter1.fasta" /> + <param name="width" value="60" /> + <output name="output" file="fasta_formatter2.out" /> + </test> + </tests> + <help> **What it does** This tool re-formats a FASTA file, changing the width of the nucleotides lines. - + **TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line. -------- @@ -84,6 +85,5 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - -</help> + </help> </tool> |
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| diff -r 1dbb5181c327 -r 9457a20156db tool_dependencies.xml --- a/tool_dependencies.xml Tue Dec 03 12:36:12 2013 -0500 +++ b/tool_dependencies.xml Mon Oct 12 10:15:31 2015 -0400 |
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| @@ -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> |