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comparison RNPxl.xml @ 0:43ddae9b94a4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:42:27 -0500
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children 3aa12d9ec7ee
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-1:000000000000 0:43ddae9b94a4
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="RNPxl" name="RNPxl" version="2.1.0">
5 <description>Tool for RNP cross linking experiment analysis.</description>
6 <macros>
7 <token name="@EXECUTABLE@">RNPxl</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>RNPxl
14
15 #if $param_in_mzML:
16 -in_mzML $param_in_mzML
17 #end if
18 #if $param_length:
19 -length $param_length
20 #end if
21 #if $param_sequence:
22 -sequence "$param_sequence"
23 #end if
24
25 #if $rep_param_target_nucleotides:
26 -target_nucleotides
27 #for token in $rep_param_target_nucleotides:
28 #if " " in str(token):
29 "$token.param_target_nucleotides"
30 #else
31 $token.param_target_nucleotides
32 #end if
33 #end for
34 #end if
35
36 #if $rep_param_mapping:
37 -mapping
38 #for token in $rep_param_mapping:
39 #if " " in str(token):
40 "$token.param_mapping"
41 #else
42 $token.param_mapping
43 #end if
44 #end for
45 #end if
46
47 #if $rep_param_restrictions:
48 -restrictions
49 #for token in $rep_param_restrictions:
50 #if " " in str(token):
51 "$token.param_restrictions"
52 #else
53 $token.param_restrictions
54 #end if
55 #end for
56 #end if
57
58 #if $rep_param_modifications:
59 -modifications
60 #for token in $rep_param_modifications:
61 #if " " in str(token):
62 "$token.param_modifications"
63 #else
64 $token.param_modifications
65 #end if
66 #end for
67 #end if
68 #if $param_peptide_mass_threshold:
69 -peptide_mass_threshold $param_peptide_mass_threshold
70 #end if
71 #if $param_precursor_variant_mz_threshold:
72 -precursor_variant_mz_threshold $param_precursor_variant_mz_threshold
73 #end if
74 #if $param_CysteineAdduct:
75 -CysteineAdduct
76 #end if
77 #if $param_in_OMSSA_ini:
78 -in_OMSSA_ini $param_in_OMSSA_ini
79 #end if
80 #if $param_in_fasta:
81 -in_fasta $param_in_fasta
82 #end if
83 #if $param_marker_ions_tolerance:
84 -marker_ions_tolerance $param_marker_ions_tolerance
85 #end if
86 #if $param_out_idXML:
87 -out_idXML $param_out_idXML
88 #end if
89 #if $param_out_csv:
90 -out_csv $param_out_csv
91 #end if
92 #if $adv_opts.adv_opts_selector=='advanced':
93 #if $adv_opts.param_continue:
94 -continue
95 #end if
96 #if $adv_opts.param_force:
97 -force
98 #end if
99 #end if
100 </command>
101 <inputs>
102 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Input file" help="(-in_mzML) "/>
103 <param name="param_length" type="integer" value="4" label="Oligonucleotide maximum length" help="(-length) "/>
104 <param name="param_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)">
105 <sanitizer>
106 <valid initial="string.printable">
107 <remove value="'"/>
108 <remove value="&quot;"/>
109 </valid>
110 </sanitizer>
111 </param>
112 <repeat name="rep_param_target_nucleotides" min="0" max="1" title="param_target_nucleotides">
113 <param name="param_target_nucleotides" type="text" size="30" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="(-target_nucleotides) e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU &lt;br&gt; or e.g. Y=C10H14N5O7PS where Y represents tG">
114 <sanitizer>
115 <valid initial="string.printable">
116 <remove value="'"/>
117 <remove value="&quot;"/>
118 </valid>
119 </sanitizer>
120 </param>
121 </repeat>
122 <repeat name="rep_param_mapping" min="0" max="1" title="param_mapping">
123 <param name="param_mapping" type="text" size="30" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help="(-mapping) ">
124 <sanitizer>
125 <valid initial="string.printable">
126 <remove value="'"/>
127 <remove value="&quot;"/>
128 </valid>
129 </sanitizer>
130 </param>
131 </repeat>
132 <repeat name="rep_param_restrictions" min="0" max="1" title="param_restrictions">
133 <param name="param_restrictions" type="text" size="30" value="A=0 C=0 U=0 G=0" label="format: target nucleotide=min_count: e.g U=1 if at least one U must be in the generated sequence" help="(-restrictions) ">
134 <sanitizer>
135 <valid initial="string.printable">
136 <remove value="'"/>
137 <remove value="&quot;"/>
138 </valid>
139 </sanitizer>
140 </param>
141 </repeat>
142 <repeat name="rep_param_modifications" min="0" max="1" title="param_modifications">
143 <param name="param_modifications" type="text" size="30" value="-H2O -H2O-HPO3 -HPO3 -H2O+HPO3 +HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help="(-modifications) ">
144 <sanitizer>
145 <valid initial="string.printable">
146 <remove value="'"/>
147 <remove value="&quot;"/>
148 </valid>
149 </sanitizer>
150 </param>
151 </repeat>
152 <param name="param_peptide_mass_threshold" type="float" value="600.0" label="Lower peptide mass (Da) threshold" help="(-peptide_mass_threshold) "/>
153 <param name="param_precursor_variant_mz_threshold" type="float" value="260.0" label="Lower m/z (Th) threshold for precursor variant" help="(-precursor_variant_mz_threshold) "/>
154 <param name="param_CysteineAdduct" display="radio" type="boolean" truevalue="-CysteineAdduct" falsevalue="" checked="false" optional="True" label="Use this flag if the +152 adduct is expected" help="(-CysteineAdduct) "/>
155 <param name="param_in_OMSSA_ini" type="data" format="txt" optional="False" label="Ini file for the OMSSA search engine" help="(-in_OMSSA_ini) "/>
156 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Fasta file for search result annotation" help="(-in_fasta) "/>
157 <param name="param_marker_ions_tolerance" type="float" value="0.05" label="mz tolerance used to determine marker ions" help="(-marker_ions_tolerance) "/>
158 <expand macro="advanced_options">
159 <param name="param_continue" display="radio" type="boolean" truevalue="-continue" falsevalue="" checked="false" optional="True" label="Do not recreate intermediate files to continue after unexpected crash" help="(-continue) "/>
160 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
161 </expand>
162 </inputs>
163 <outputs>
164 <data name="param_out_idXML" format="idxml"/>
165 <data name="param_out_csv" format="tabular"/>
166 </outputs>
167 <help>Tool for RNP cross linking experiment analysis.
168
169
170 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxl.html</help>
171 </tool>