Mercurial > repos > galaxyp > openms_rnadigestor

comparison RNADigestor.xml @ 0:3e7d3f64392b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:14:58 +0000
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children 88969677ae51
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-1:000000000000 0:3e7d3f64392b
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Digests an RNA sequence database in-silico.</description>
6 <macros>
7 <token name="@EXECUTABLE@">RNADigestor</token>
8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros>
12 <expand macro="requirements"/>
13 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@
16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out &&
22
23 ## Main program call
24
25 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
31 -out
32 'out/output.${gxy2omsext("fasta")}'
33
34 ## Postprocessing
35 && mv 'out/output.${gxy2omsext("fasta")}' '$out'
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
38 #end if]]></command>
39 <configfiles>
40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles>
43 <inputs>
44 <param name="in" argument="-in" type="data" format="fasta" optional="false" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
45 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
46 <param name="min_length" argument="-min_length" type="integer" optional="true" value="3" label="Minimum length of a fragment" help=""/>
47 <param name="max_length" argument="-max_length" type="integer" optional="true" value="30" label="Maximum length of a fragment" help=""/>
48 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="Digestion enzyme (RNase)" help="">
49 <option value="RNase_T1" selected="true">RNase_T1</option>
50 <option value="RNase_MC1">RNase_MC1</option>
51 <option value="RNase_H">RNase_H</option>
52 <option value="no cleavage">no cleavage</option>
53 <option value="unspecific cleavage">unspecific cleavage</option>
54 <option value="cusativin">cusativin</option>
55 <option value="RNase_U2">RNase_U2</option>
56 <option value="RNase_A">RNase_A</option>
57 <expand macro="list_string_san"/>
58 </param>
59 <param name="unique" argument="-unique" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Report each unique sequence fragment only once" help=""/>
60 <param name="cdna" argument="-cdna" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Input file contains cDNA sequences - replace 'T' with 'U')" help=""/>
61 <expand macro="adv_opts_macro">
62 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
63 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
64 <expand macro="list_string_san"/>
65 </param>
66 </expand>
67 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
69 </param>
70 </inputs>
71 <outputs>
72 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
75 </data>
76 </outputs>
77 <tests>
78 <expand macro="autotest_RNADigestor"/>
79 <expand macro="manutest_RNADigestor"/>
80 </tests>
81 <help><![CDATA[Digests an RNA sequence database in-silico.
82
83
84 For more information, visit http://www.openms.de/documentation/UTILS_RNADigestor.html]]></help>
85 <expand macro="references"/>
86 </tool>