Mercurial > repos > cpt > cpt_psm_prep
diff cpt_psm_prep/cpt_psm_0_prep.xml @ 0:e4de0a0e90c8 draft
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author | cpt |
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date | Tue, 05 Jul 2022 05:38:34 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_psm_prep/cpt_psm_0_prep.xml Tue Jul 05 05:38:34 2022 +0000 @@ -0,0 +1,63 @@ +<?xml version="1.0"?> +<tool id="PSM.Prep" name="PSM Prep" version="1.94.2"> + <description>prepares data for the PSM Plotter</description> + <version_command>perl cpt_psm_0_prep.pl --version</version_command> + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + <requirements> + <requirement type="package" version="5.22.1">perl</requirement> + <requirement type="package">perl-bioperl</requirement> + <requirement type="package">perl-moose</requirement> + <requirement type="package">perl-ipc-run</requirement> + <requirement type="package">perl-getopt-long-descriptive</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +perl -Mlib=$__tool_directory__/lib $__tool_directory__/cpt_psm_0_prep.pl +--galaxy +--outfile_supporting $__new_file_path__ +#for $item in $repeat_file: +--file "${item.file}" +#end for + +--cpt_psm_object "${cpt_psm_object}" + +--cpt_psm_object_files_path "${cpt_psm_object.files_path}" + +--cpt_psm_object_format "${cpt_psm_object_format}" + +--cpt_psm_object_id "${cpt_psm_object.id}" + +]]></command> + <inputs> + <repeat name="repeat_file" title="File"> + <param name="file" help="Input file" optional="False" label="file" type="data"/> + </repeat> + <param name="cpt_psm_object_format" help="Output PSM Object" optional="False" label="Format of cpt_psm_object" type="select"> + <option value="TXT" selected="True">TXT</option> + <option value="CONF">CONF</option> + </param> + </inputs> + <outputs> + <data name="cpt_psm_object" format="TXT"> + <change_format> + <when input="cpt_psm_object_format" value="TXT" format="txt"/> + <when input="cpt_psm_object_format" value="CONF" format="txt"/> + </change_format> + </data> + </outputs> + <help>NAME +==== + +PSM Prep + +DESCRIPTION +=========== + +This tool takes in 2 or more GenBank files, blasts, and prepares data +structures for use in the companion tool: PSM Plotter. Select as many +(multi)-gbk files as you *might* want to plot. Once this tool is done, +you can select any subset of those to plot then. +</help> + <tests/> +</tool>