Mercurial > repos > cpt > cpt_psm_prep

comparison cpt_psm_0_prep.xml @ 1:d724f34e671d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:50:07 +0000
parents
children
comparison
equal deleted inserted replaced
0:e4de0a0e90c8 1:d724f34e671d
1 <tool id="PSM.Prep" name="PSM Prep" version="1.94.2">
2 <description>prepares data for the PSM Plotter</description>
3 <version_command>perl cpt_psm_0_prep.pl --version</version_command>
4 <stdio>
5 <exit_code range="1:" level="fatal"/>
6 </stdio>
7 <requirements>
8 <requirement type="package" version="5.22.1">perl</requirement>
9 <requirement type="package">perl-bioperl</requirement>
10 <requirement type="package">perl-moose</requirement>
11 <requirement type="package">perl-ipc-run</requirement>
12 <requirement type="package">perl-getopt-long-descriptive</requirement>
13 </requirements>
14 <command detect_errors="aggressive"><![CDATA[
15 perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_0_prep.pl'
16 --galaxy
17 --outfile_supporting '$__new_file_path__'
18 #for $item in $repeat_file:
19 --file "${item.file}"
20 #end for
21
22 --cpt_psm_object "${cpt_psm_object}"
23
24 --cpt_psm_object_files_path "${cpt_psm_object.files_path}"
25
26 --cpt_psm_object_format "${cpt_psm_object_format}"
27
28 --cpt_psm_object_id "${cpt_psm_object.id}"
29
30 ]]></command>
31 <inputs>
32 <repeat name="repeat_file" title="File">
33 <param name="file" help="Input file" optional="False" label="file" type="data"/>
34 </repeat>
35 <param name="cpt_psm_object_format" help="Output PSM Object" optional="False" label="Format of cpt_psm_object" type="select">
36 <option value="TXT" selected="True">TXT</option>
37 <option value="CONF">CONF</option>
38 </param>
39 </inputs>
40 <outputs>
41 <data name="cpt_psm_object" format="TXT">
42 <change_format>
43 <when input="cpt_psm_object_format" value="TXT" format="txt"/>
44 <when input="cpt_psm_object_format" value="CONF" format="txt"/>
45 </change_format>
46 </data>
47 </outputs>
48 <help>NAME
49 ====
50
51 PSM Prep
52
53 DESCRIPTION
54 ===========
55
56 This tool takes in 2 or more GenBank files, blasts, and prepares data
57 structures for use in the companion tool: PSM Plotter. Select as many
58 (multi)-gbk files as you *might* want to plot. Once this tool is done,
59 you can select any subset of those to plot then.
60 </help>
61 <tests/>
62 </tool>