Mercurial > repos > galaxyp > openms_masscalculator

comparison MassCalculator.xml @ 11:65c6e741ddf3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:13:07 +0000
parents ff18cb79cdd2
children bcd50cd4fe42
comparison
equal deleted inserted replaced
10:edb4ca47bad8 11:65c6e741ddf3
34 -in 34 -in
35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
36 #end if 36 #end if
37 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 37 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
38 -out 38 -out
39 'out/output.${gxy2omsext("txt")}' 39 'out/output.${gxy2omsext("csv")}'
40 #end if 40 #end if
41 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 41 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
42 | tee '$stdout' 42 | tee '$stdout'
43 #end if 43 #end if
44 44
45 ## Postprocessing 45 ## Postprocessing
46 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 46 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 && mv 'out/output.${gxy2omsext("txt")}' '$out' 47 && mv 'out/output.${gxy2omsext("csv")}' '$out'
48 #end if 48 #end if
49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
50 && mv '@EXECUTABLE@.ctd' '$ctd_out' 50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
51 #end if]]></command> 51 #end if]]></command>
52 <configfiles> 52 <configfiles>
53 <inputs name="args_json" data_style="paths"/> 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> 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
55 </configfiles> 55 </configfiles>
56 <inputs> 56 <inputs>
57 <param name="in" argument="-in" type="data" format="txt" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/> 57 <param name="in" argument="-in" type="data" format="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/>
58 <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 58 <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide 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"/> 59 <expand macro="list_string_val"/>
60 <expand macro="list_string_san"/> 60 <expand macro="list_string_san"/>
61 </param> 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)"> 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)">
85 </param> 85 </param>
86 <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=""> 86 <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="">
87 <expand macro="list_string_san"/> 87 <expand macro="list_string_san"/>
88 </param> 88 </param>
89 <expand macro="adv_opts_macro"> 89 <expand macro="adv_opts_macro">
90 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 90 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
91 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 91 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
92 <expand macro="list_string_san"/> 92 <expand macro="list_string_san"/>
93 </param> 93 </param>
94 </expand> 94 </expand>
95 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
96 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option> 96 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
97 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 97 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
98 </param> 98 </param>
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"> 101 <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
102 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> 102 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
103 </data> 103 </data>
104 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> 104 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
105 <filter>OPTIONAL_OUTPUTS is None</filter> 105 <filter>OPTIONAL_OUTPUTS is None</filter>
106 </data> 106 </data>
113 <expand macro="manutest_MassCalculator"/> 113 <expand macro="manutest_MassCalculator"/>
114 </tests> 114 </tests>
115 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences 115 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
116 116
117 117
118 For more information, visit http://www.openms.de/documentation/UTILS_MassCalculator.html]]></help> 118 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MassCalculator.html]]></help>
119 <expand macro="references"/> 119 <expand macro="references"/>
120 </tool> 120 </tool>