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comparison RNADigestor.xml @ 4:c951784e4967 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:19:16 +0000
parents 88969677ae51
children ef145c9fb233
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3:6d492588ae83 4:c951784e4967
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Digests an RNA sequence database in-silico.</description> 5 <description>Digests an RNA sequence database in-silico.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RNADigestor</token> 7 <token name="@EXECUTABLE@">RNADigestor</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <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)"/> 42 <param 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=""/> 43 <param 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=""/> 44 <param 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=""/> 45 <param 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=""> 46 <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme (RNase)" help="">
49 <option value="RNase_T1" selected="true">RNase_T1</option>
50 <option value="RNase_H">RNase_H</option>
51 <option value="no cleavage">no cleavage</option>
52 <option value="unspecific cleavage">unspecific cleavage</option>
53 <option value="cusativin">cusativin</option>
54 <option value="RNase_U2">RNase_U2</option> 47 <option value="RNase_U2">RNase_U2</option>
55 <option value="RNase_A">RNase_A</option> 48 <option value="RNase_A">RNase_A</option>
56 <option value="RNase_MC1">RNase_MC1</option> 49 <option value="RNase_MC1">RNase_MC1</option>
57 <expand macro="list_string_san"/> 50 <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>
54 <option value="colicin_E5">colicin_E5</option>
55 <option value="no cleavage">no cleavage</option>
56 <option value="unspecific cleavage">unspecific cleavage</option>
57 <expand macro="list_string_san" name="enzyme"/>
58 </param> 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=""/> 59 <param 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=""/> 60 <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"> 61 <expand macro="adv_opts_macro">
62 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 62 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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=""> 63 <param 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"/> 64 <expand macro="list_string_san" name="test"/>
65 </param> 65 </param>
66 </expand> 66 </expand>
67 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 67 <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> 68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
69 </param> 69 </param>
72 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/> 72 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
75 </data> 75 </data>
76 </outputs> 76 </outputs>
77 <tests> 77 <tests><test expect_num_outputs="1"><!--random RNAsequence input -->
78 <expand macro="autotest_RNADigestor"/> 78 <param name="adv_opts|test" value="true"/>
79 <expand macro="manutest_RNADigestor"/> 79 <param name="in" ftype="fasta" value="random_RNA.fa"/>
80 </tests> 80 <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
81 </test>
82 </tests>
81 <help><![CDATA[Digests an RNA sequence database in-silico. 83 <help><![CDATA[Digests an RNA sequence database in-silico.
82 84
83 85
84 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RNADigestor.html]]></help> 86 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNADigestor.html]]></help>
85 <expand macro="references"/> 87 <expand macro="references"/>
86 </tool> 88 </tool>