Mercurial > repos > galaxyp > openms_rnamasscalculator

comparison RNAMassCalculator.xml @ 0:4f8478024146 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:05:38 +0000
parents
children f8475273db10
comparison
equal deleted inserted replaced
-1:000000000000 0:4f8478024146
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="RNAMassCalculator" name="RNAMassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Calculates masses and mass-to-charge ratios of RNA sequences</description>
6 <macros>
7 <token name="@EXECUTABLE@">RNAMassCalculator</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 #if $in:
20 mkdir in &&
21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
22 #end if
23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
24 mkdir out &&
25 #end if
26
27 ## Main program call
28
29 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 #if $in:
34 -in
35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
36 #end if
37 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
38 -out
39 'out/output.${gxy2omsext("txt")}'
40 #end if
41 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
42 | tee '$stdout'
43 #end if
44
45 ## Postprocessing
46 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 && mv 'out/output.${gxy2omsext("txt")}' '$out'
48 #end if
49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
51 #end if]]></command>
52 <configfiles>
53 <inputs name="args_json" data_style="paths"/>
54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
55 </configfiles>
56 <inputs>
57 <param name="in" argument="-in" type="data" format="txt" optional="true" label="Input file with RNA sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/>
58 <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of RNA sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
59 <expand macro="list_string_val"/>
60 <expand macro="list_string_san"/>
61 </param>
62 <param name="charge" argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
63 <expand macro="list_integer_valsan"/>
64 </param>
65 <param name="format" argument="-format" display="radio" type="select" optional="false" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
66 <option value="list" selected="true">list</option>
67 <option value="table">table</option>
68 <option value="mass_only">mass_only</option>
69 <option value="mz_only">mz_only</option>
70 <expand macro="list_string_san"/>
71 </param>
72 <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) oligonucleotide masses" help=""/>
73 <param name="fragment_type" argument="-fragment_type" type="select" optional="false" label="For what type of sequence/fragment the mass should be computed" help="">
74 <option value="full" selected="true">full</option>
75 <option value="internal">internal</option>
76 <option value="5-prime">5-prime</option>
77 <option value="3-prime">3-prime</option>
78 <option value="a-B-ion">a-B-ion</option>
79 <option value="a-ion">a-ion</option>
80 <option value="b-ion">b-ion</option>
81 <option value="c-ion">c-ion</option>
82 <option value="d-ion">d-ion</option>
83 <option value="w-ion">w-ion</option>
84 <option value="x-ion">x-ion</option>
85 <option value="y-ion">y-ion</option>
86 <option value="z-ion">z-ion</option>
87 <expand macro="list_string_san"/>
88 </param>
89 <param name="separator" argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
90 <expand macro="list_string_san"/>
91 </param>
92 <expand macro="adv_opts_macro">
93 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
94 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
95 <expand macro="list_string_san"/>
96 </param>
97 </expand>
98 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
99 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
100 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
101 </param>
102 </inputs>
103 <outputs>
104 <data name="out" label="${tool.name} on ${on_string}: out" format="txt">
105 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
106 </data>
107 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
108 <filter>OPTIONAL_OUTPUTS is None</filter>
109 </data>
110 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
111 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
112 </data>
113 </outputs>
114 <tests>
115 <expand macro="autotest_RNAMassCalculator"/>
116 <expand macro="manutest_RNAMassCalculator"/>
117 </tests>
118 <help><![CDATA[Calculates masses and mass-to-charge ratios of RNA sequences
119
120
121 For more information, visit http://www.openms.de/documentation/UTILS_RNAMassCalculator.html]]></help>
122 <expand macro="references"/>
123 </tool>