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comparison RNADigestor.xml @ 5:ef145c9fb233 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:46:15 +0000
parents c951784e4967
children
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4:c951784e4967 5:ef145c9fb233
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [RNA]-->
4 <tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Digests an RNA sequence database in-silico.</description> 4 <description>Digests an RNA sequence database in-silico</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">RNADigestor</token> 6 <token name="@EXECUTABLE@">RNADigestor</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="fasta" optional="false" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/> 41 <param argument="-in" type="data" format="fasta" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
43 <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/> 42 <param argument="-missed_cleavages" type="integer" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
44 <param argument="-min_length" type="integer" optional="true" value="3" label="Minimum length of a fragment" help=""/> 43 <param argument="-min_length" type="integer" value="3" label="Minimum length of a fragment" help=""/>
45 <param argument="-max_length" type="integer" optional="true" value="30" label="Maximum length of a fragment" help=""/> 44 <param argument="-max_length" type="integer" value="30" label="Maximum length of a fragment" help=""/>
46 <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme (RNase)" help=""> 45 <param argument="-enzyme" type="select" label="Digestion enzyme (RNase)" help="">
47 <option value="RNase_U2">RNase_U2</option> 46 <option value="RNase_T1" selected="true">RNase_T1</option>
48 <option value="RNase_A">RNase_A</option>
49 <option value="RNase_MC1">RNase_MC1</option>
50 <option value="RNase_H">RNase_H</option> 47 <option value="RNase_H">RNase_H</option>
51 <option value="cusativin">cusativin</option>
52 <option value="RNase_T1" selected="true">RNase_T1</option>
53 <option value="mazF">mazF</option> 48 <option value="mazF">mazF</option>
54 <option value="colicin_E5">colicin_E5</option> 49 <option value="colicin_E5">colicin_E5</option>
50 <option value="RNase_MC1">RNase_MC1</option>
51 <option value="RNase_A">RNase_A</option>
52 <option value="RNase_U2">RNase_U2</option>
53 <option value="cusativin">cusativin</option>
55 <option value="no cleavage">no cleavage</option> 54 <option value="no cleavage">no cleavage</option>
56 <option value="unspecific cleavage">unspecific cleavage</option> 55 <option value="unspecific cleavage">unspecific cleavage</option>
57 <expand macro="list_string_san" name="enzyme"/> 56 <expand macro="list_string_san" name="enzyme"/>
58 </param> 57 </param>
59 <param argument="-unique" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Report each unique sequence fragment only once" help=""/> 58 <param argument="-unique" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Report each unique sequence fragment only once" help=""/>
60 <param argument="-cdna" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Input file contains cDNA sequences - replace 'T' with 'U')" help=""/> 59 <param 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"> 60 <expand macro="adv_opts_macro">
62 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 61 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
63 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 62 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
64 <expand macro="list_string_san" name="test"/> 63 <expand macro="list_string_san" name="test"/>
65 </param> 64 </param>
66 </expand> 65 </expand>
67 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 66 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
72 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/> 71 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
75 </data> 74 </data>
76 </outputs> 75 </outputs>
77 <tests><test expect_num_outputs="1"><!--random RNAsequence input --> 76 <tests>
78 <param name="adv_opts|test" value="true"/> 77 <test expect_num_outputs="1">
79 <param name="in" ftype="fasta" value="random_RNA.fa"/> 78 <!--random RNAsequence input -->
80 <output name="out" ftype="fasta" value="RNADigestor.fasta"/> 79 <param name="adv_opts|test" value="true"/>
81 </test> 80 <param name="in" ftype="fasta" value="random_RNA.fa"/>
82 </tests> 81 <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
82 </test>
83 </tests>
83 <help><![CDATA[Digests an RNA sequence database in-silico. 84 <help><![CDATA[Digests an RNA sequence database in-silico.
84 85
85 86
86 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNADigestor.html]]></help> 87 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNADigestor.html]]></help>
87 <expand macro="references"/> 88 <expand macro="references"/>
88 </tool> 89 </tool>