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comparison MetaProSIP.xml @ 6:96cc79adfadb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 14:37:53 -0400
parents fdb3fbfef4cc
children 8febc104e78c
comparison
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5:fdb3fbfef4cc 6:96cc79adfadb
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="MetaProSIP" name="MetaProSIP" version="2.3.0"> 4 <tool id="MetaProSIP" name="MetaProSIP" version="2.3.1">
5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description> 5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MetaProSIP</token> 7 <token name="@EXECUTABLE@">MetaProSIP</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"> 10 <expand macro="requirements">
13 <requirement type="package" version="3.4.1">r-base</requirement> 11 <requirement type="package" version="3.4.1">r-base</requirement>
12 <requirement type="package" version="3.0.1">r-gplots</requirement>
14 </expand> 13 </expand>
15 <command>MetaProSIP 14 <expand macro="stdio"/>
15 <command><![CDATA[
16 MetaProSIP
16 17
17 #if $param_in_mzML: 18 #if $param_in_mzML:
18 -in_mzML $param_in_mzML 19 -in_mzML $param_in_mzML
19 #end if 20 #end if
20 #if $param_in_fasta: 21 #if $param_in_fasta:
56 "$param_plot_extension" 57 "$param_plot_extension"
57 #else 58 #else
58 $param_plot_extension 59 $param_plot_extension
59 #end if 60 #end if
60 #end if 61 #end if
61 #if $param_qc_output_directory: 62 #if $param_plot_extension == 'pdf':
62 -qc_output_directory "$param_qc_output_directory" 63 -qc_output_directory images
64 #else
65 -qc_output_directory '${html_file.files_path}'
63 #end if 66 #end if
64 #if $param_labeling_element: 67 #if $param_labeling_element:
65 -labeling_element 68 -labeling_element
66 #if " " in str($param_labeling_element): 69 #if " " in str($param_labeling_element):
67 "$param_labeling_element" 70 "$param_labeling_element"
125 #end if 128 #end if
126 #if $adv_opts.param_force: 129 #if $adv_opts.param_force:
127 -force 130 -force
128 #end if 131 #end if
129 #end if 132 #end if
130 </command> 133 -threads "\${GALAXY_SLOTS:-1}"
134
135 ## remove urls and paths (keeping the file name basename)
136 && sed -i -e 's/file:\/\/[^[:space:]]\+\///g; s/\/[^[:space:]]\+\///g' $param_out_csv
137
138 ## get html file (should be only one [?])
139 #if $param_plot_extension != 'pdf':
140 && cp '${html_file.files_path}'/*\.html output.html
141 #end if
142 ]]></command>
131 <inputs> 143 <inputs>
132 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/> 144 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
133 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/> 145 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
134 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/> 146 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
135 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/> 147 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
141 <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/> 153 <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
142 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) "> 154 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
143 <option value="png" selected="true">png</option> 155 <option value="png" selected="true">png</option>
144 <option value="svg">svg</option> 156 <option value="svg">svg</option>
145 <option value="pdf">pdf</option> 157 <option value="pdf">pdf</option>
146 </param>
147 <param name="param_qc_output_directory" type="text" size="30" label="Output directory for the quality report" help="(-qc_output_directory) ">
148 <sanitizer>
149 <valid initial="string.printable">
150 <remove value="'"/>
151 <remove value="&quot;"/>
152 </valid>
153 </sanitizer>
154 </param> 158 </param>
155 <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) "> 159 <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
156 <option value="C" selected="true">C</option> 160 <option value="C" selected="true">C</option>
157 <option value="N">N</option> 161 <option value="N">N</option>
158 <option value="H">H</option> 162 <option value="H">H</option>
180 <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/> 184 <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/>
181 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 185 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
182 </expand> 186 </expand>
183 </inputs> 187 </inputs>
184 <outputs> 188 <outputs>
185 <data name="param_out_csv" format="tabular"/> 189 <data name="param_out_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/>
186 <data name="param_out_peptide_centric_csv" format="tabular"/> 190 <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/>
191 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage">
192 <filter>param_plot_extension == 'png' or param_plot_extension == 'svg'</filter>
193 </data>
194 <collection name="images" type="list" label="${tool.name} on ${on_string}: images">
195 <filter>param_plot_extension == 'pdf'</filter>
196 <discover_datasets pattern="__name_and_ext__" directory="images" />
197 </collection>
187 </outputs> 198 </outputs>
199 <tests>
200 <test>
201 <param name="param_in_mzML" value="MetaProSIP_1_input.mzML"/>
202 <param name="param_in_fasta" value="MetaProSIP_1_input.fasta"/>
203 <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML"/>
204 <output name="param_out_csv" file="MetaProSIP_1_output_1.csv" />
205 <output name="param_out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" />
206 </test>
207 </tests>
188 <help>Performs proteinSIP on peptide features for elemental flux analysis. 208 <help>Performs proteinSIP on peptide features for elemental flux analysis.
189 209
190 210
191 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html</help> 211 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html</help>
212 <expand macro="references"/>
192 </tool> 213 </tool>