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comparison MassCalculator.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="MassCalculator" name="MassCalculator" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="MassCalculator" name="MassCalculator" version="2.0.0">
5 <token name="@EXECUTABLE@">MassCalculator</token> 5 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">MassCalculator</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>MassCalculator 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MassCalculator
11 14
12 -in ${param_in} 15 #if $param_in:
13 -in_seq ${param_in_seq} 16 -in $param_in
14 -out ${param_out} 17 #end if
15 -charge ${param_charge} 18
16 -format ${param_format} 19 #if $rep_param_in_seq:
17 ${param_average_mass} 20 -in_seq
18 -fragment_type ${param_fragment_type} 21 #for token in $rep_param_in_seq:
19 -separator ${param_separator} 22 #if &quot; &quot; in str(token):
20 -threads \${GALAXY_SLOTS:-24} 23 &quot;$token.param_in_seq&quot;
24 #else
25 $token.param_in_seq
26 #end if
27 #end for
28 #end if
29 #if $param_out:
30 -out $param_out
31 #end if
32
33 #if $rep_param_charge:
34 -charge
35 #for token in $rep_param_charge:
36 #if &quot; &quot; in str(token):
37 &quot;$token.param_charge&quot;
38 #else
39 $token.param_charge
40 #end if
41 #end for
42 #end if
43 #if $param_format:
44 -format
45 #if &quot; &quot; in str($param_format):
46 &quot;$param_format&quot;
47 #else
48 $param_format
49 #end if
50 #end if
51 #if $param_average_mass:
52 -average_mass
53 #end if
54 #if $param_fragment_type:
55 -fragment_type
56 #if &quot; &quot; in str($param_fragment_type):
57 &quot;$param_fragment_type&quot;
58 #else
59 $param_fragment_type
60 #end if
61 #end if
62 #if $param_separator:
63 -separator &quot;$param_separator&quot;
64 #end if
65 -threads \${GALAXY_SLOTS:-24}
66 #if $adv_opts.adv_opts_selector=='advanced':
67 #if $adv_opts.param_force:
68 -force
69 #end if
70 #end if
21 </command> 71 </command>
22 <inputs> 72 <inputs>
23 <param name="param_in" type="data" format="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in)"/> 73 <param format="txt" help="(-in) " label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" name="param_in" optional="True" type="data"/>
24 <param name="param_in_seq" type="text" size="20" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq)"/> 74 <repeat min="0" name="rep_param_in_seq" title="param_in_seq">
25 <param name="param_charge" type="text" size="20" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge)"/> 75 <param help="(-in_seq) " label="List of peptide sequences (mutually exclusive to 'in')" name="param_in_seq" size="30" type="text">
26 <param name="param_format" type="select" optional="True" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)#br#" help="(-format)"> 76 <sanitizer>
27 <option value="list">list</option> 77 <valid initial="string.printable">
28 <option value="table">table</option> 78 <remove value="'"/>
29 <option value="mass_only">mass_only</option> 79 <remove value="&quot;"/>
30 <option value="mz_only">mz_only</option> 80 </valid>
31 </param> 81 </sanitizer>
32 <param name="param_average_mass" type="boolean" truevalue="-average_mass true" falsevalue="-average_mass false" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass)"/> 82 </param>
33 <param name="param_fragment_type" type="select" optional="True" value="full" label="For what type of sequence/fragment the mass should be computed#br#" help="(-fragment_type)"> 83 </repeat>
34 <option value="full">full</option> 84 <repeat max="1" min="0" name="rep_param_charge" title="param_charge">
35 <option value="internal">internal</option> 85 <param help="(-charge) " label="List of charge states; required if 'in_seq' is given" name="param_charge" size="30" type="text" value="0">
36 <option value="N-terminal">N-terminal</option> 86 <sanitizer>
37 <option value="C-terminal">C-terminal</option> 87 <valid initial="string.printable">
38 <option value="a-ion">a-ion</option> 88 <remove value="'"/>
39 <option value="b-ion">b-ion</option> 89 <remove value="&quot;"/>
40 <option value="c-ion">c-ion</option> 90 </valid>
41 <option value="x-ion">x-ion</option> 91 </sanitizer>
42 <option value="y-ion">y-ion</option> 92 </param>
43 <option value="z-ion">z-ion</option> 93 </repeat>
44 </param> 94 <param help="(-format) " label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" name="param_format" optional="True" type="select" value="list">
45 <param name="param_separator" type="text" size="20" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator)"/> 95 <option value="list">list</option>
46 </inputs> 96 <option value="table">table</option>
47 <outputs> 97 <option value="mass_only">mass_only</option>
48 <data name="param_out" label="Output file; if empty, output is written to the screen" format="txt"/> 98 <option value="mz_only">mz_only</option>
49 </outputs> 99 </param>
50 <help>**What it does** 100 <param checked="false" falsevalue="" help="(-average_mass) " label="Compute average (instead of monoisotopic) peptide masses" name="param_average_mass" optional="True" truevalue="-average_mass" type="boolean"/>
51 101 <param help="(-fragment_type) " label="For what type of sequence/fragment the mass should be computed" name="param_fragment_type" optional="True" type="select" value="full">
52 Calculates masses and mass-to-charge ratios of peptide sequences 102 <option value="full">full</option>
103 <option value="internal">internal</option>
104 <option value="N-terminal">N-terminal</option>
105 <option value="C-terminal">C-terminal</option>
106 <option value="a-ion">a-ion</option>
107 <option value="b-ion">b-ion</option>
108 <option value="c-ion">c-ion</option>
109 <option value="x-ion">x-ion</option>
110 <option value="y-ion">y-ion</option>
111 <option value="z-ion">z-ion</option>
112 </param>
113 <param help="(-separator) " label="Field separator for 'table' output format; by default, the 'tab' character is used" name="param_separator" size="30" type="text">
114 <sanitizer>
115 <valid initial="string.printable">
116 <remove value="'"/>
117 <remove value="&quot;"/>
118 </valid>
119 </sanitizer>
120 </param>
121 <expand macro="advanced_options">
122 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
123 </expand>
124 </inputs>
125 <outputs>
126 <data format="txt" name="param_out"/>
127 </outputs>
128 <help>Calculates masses and mass-to-charge ratios of peptide sequences
53 129
54 130
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html 131 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html</help>
56 132 </tool>
57 @REFERENCES@
58 </help>
59 </tool>