Mercurial > repos > galaxyp > openms_metaprosip

comparison MetaProSIP.xml @ 7:8febc104e78c 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 f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:02:33 -0400
parents 96cc79adfadb
children 73c1493ac4c2
comparison
equal deleted inserted replaced
6:96cc79adfadb 7:8febc104e78c
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="2.3.1"> 4 <tool id="MetaProSIP" name="MetaProSIP" version="2.3.2">
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="requirements"> 10 <expand macro="requirements">
11 <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> 12 <requirement type="package" version="3.0.1">r-gplots</requirement>
13 </expand> 13 </expand>
14 <expand macro="stdio"/> 14 <expand macro="stdio"/>
15 <command><![CDATA[ 15 <command detect_errors="aggressive"><![CDATA[
16 MetaProSIP 16 MetaProSIP
17 17
18 #if $param_in_mzML: 18 #if $param_in_mzML:
19 -in_mzML $param_in_mzML 19 -in_mzML $param_in_mzML
20 #end if 20 #end if
23 #end if 23 #end if
24 #if $param_out_csv: 24 #if $param_out_csv:
25 -out_csv $param_out_csv 25 -out_csv $param_out_csv
26 #end if 26 #end if
27 #if $param_out_peptide_centric_csv: 27 #if $param_out_peptide_centric_csv:
28 -out_peptide_centric_csv $param_out_peptide_centric_csv 28 -out_peptide_centric_csv param_out_peptide_centric_csv
29 #end if 29 #end if
30 #if $param_in_featureXML: 30 #if $param_in_featureXML:
31 -in_featureXML $param_in_featureXML 31 -in_featureXML $param_in_featureXML
32 #end if 32 #end if
33 #if $param_mz_tolerance_ppm: 33 #if $param_mz_tolerance_ppm:
57 "$param_plot_extension" 57 "$param_plot_extension"
58 #else 58 #else
59 $param_plot_extension 59 $param_plot_extension
60 #end if 60 #end if
61 #end if 61 #end if
62 #if $param_plot_extension == 'pdf': 62 -qc_output_directory images
63 -qc_output_directory images
64 #else
65 -qc_output_directory '${html_file.files_path}'
66 #end if
67 #if $param_labeling_element: 63 #if $param_labeling_element:
68 -labeling_element 64 -labeling_element
69 #if " " in str($param_labeling_element): 65 #if " " in str($param_labeling_element):
70 "$param_labeling_element" 66 "$param_labeling_element"
71 #else 67 #else
130 -force 126 -force
131 #end if 127 #end if
132 #end if 128 #end if
133 -threads "\${GALAXY_SLOTS:-1}" 129 -threads "\${GALAXY_SLOTS:-1}"
134 130
135 ## remove urls and paths (keeping the file name basename) 131 ## - add comment char to first line,
136 && sed -i -e 's/file:\/\/[^[:space:]]\+\///g; s/\/[^[:space:]]\+\///g' $param_out_csv 132 ## - remove leading/trailing spaces in fields
133 ## - remove empty line(s)
134 ## - remove 'file://' and get basename of filenames in the table
135 ## - add empty fields as '0' (MetaproSIP output has varying number of output columns, ie it omits the last columns if there are no values)
136 && cat param_out_peptide_centric_csv |
137 sed '1 s/^/#/' |
138 sed 's/\t /\t/g; s/ \t/\t/g; s/ /_/g' |
139 grep -v "^$" |
140 sed "s/\tfile:\/\//\t/g; s/\t\/[^\t]\+\//\t/g; s/\.$param_plot_extension//g" |
141 awk -v FS='\t' 'BEGIN{line=0}{if(line==0){ncol=NF; print $0}else{printf("%s",$0); for(i=0; i<ncol-NF; i++){printf("\t0")}printf("\n")}line+=1}' > "$param_out_peptide_centric_csv"
137 142
138 ## get html file (should be only one [?]) 143 ## get html file (should be only one [?])
139 #if $param_plot_extension != 'pdf': 144
140 && cp '${html_file.files_path}'/*\.html output.html 145 #if $param_collection or $param_plot_extension == 'pdf'
146 && rm -f images/*\.html
147 #else
148 && mv images/*\.html '${html_file}'
149 && mv images/ '${html_file.files_path}'
141 #end if 150 #end if
142 ]]></command> 151 ]]></command>
143 <inputs> 152 <inputs>
144 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/> 153 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
145 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/> 154 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
165 <param name="param_use_unassigned_ids" display="radio" type="boolean" truevalue="-use_unassigned_ids" falsevalue="" checked="false" optional="True" label="Include identifications not assigned to a feature in pattern detection" help="(-use_unassigned_ids) "/> 174 <param name="param_use_unassigned_ids" display="radio" type="boolean" truevalue="-use_unassigned_ids" falsevalue="" checked="false" optional="True" label="Include identifications not assigned to a feature in pattern detection" help="(-use_unassigned_ids) "/>
166 <param name="param_use_averagine_ids" display="radio" type="boolean" truevalue="-use_averagine_ids" falsevalue="" checked="false" optional="True" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help="(-use_averagine_ids) "/> 175 <param name="param_use_averagine_ids" display="radio" type="boolean" truevalue="-use_averagine_ids" falsevalue="" checked="false" optional="True" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help="(-use_averagine_ids) "/>
167 <param name="param_report_natural_peptides" display="radio" type="boolean" truevalue="-report_natural_peptides" falsevalue="" checked="false" optional="True" label="Whether purely natural peptides are reported in the quality report" help="(-report_natural_peptides) "/> 176 <param name="param_report_natural_peptides" display="radio" type="boolean" truevalue="-report_natural_peptides" falsevalue="" checked="false" optional="True" label="Whether purely natural peptides are reported in the quality report" help="(-report_natural_peptides) "/>
168 <param name="param_filter_monoisotopic" display="radio" type="boolean" truevalue="-filter_monoisotopic" falsevalue="" checked="false" optional="True" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help="(-filter_monoisotopic) "/> 177 <param name="param_filter_monoisotopic" display="radio" type="boolean" truevalue="-filter_monoisotopic" falsevalue="" checked="false" optional="True" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help="(-filter_monoisotopic) "/>
169 <param name="param_cluster" display="radio" type="boolean" truevalue="-cluster" falsevalue="" checked="false" optional="True" label="Perform grouping" help="(-cluster) "/> 178 <param name="param_cluster" display="radio" type="boolean" truevalue="-cluster" falsevalue="" checked="false" optional="True" label="Perform grouping" help="(-cluster) "/>
179 <param name="param_collection" type="boolean" checked="true" label="output images as collection" help="if enabled images are written to a collection amd to a webpage otherwise (pdf is always written to a collection)"/>
170 <expand macro="advanced_options"> 180 <expand macro="advanced_options">
171 <param name="param_min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="(-min_correlation_distance_to_averagine) Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/> 181 <param name="param_min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="(-min_correlation_distance_to_averagine) Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
172 <param name="param_pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_15N_TIC_threshold) "/> 182 <param name="param_pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_15N_TIC_threshold) "/>
173 <param name="param_pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_13C_TIC_threshold) "/> 183 <param name="param_pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_13C_TIC_threshold) "/>
174 <param name="param_pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_2H_TIC_threshold) "/> 184 <param name="param_pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_2H_TIC_threshold) "/>
186 </expand> 196 </expand>
187 </inputs> 197 </inputs>
188 <outputs> 198 <outputs>
189 <data name="param_out_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/> 199 <data name="param_out_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/>
190 <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/> 200 <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/>
191 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage"> 201 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage">
192 <filter>param_plot_extension == 'png' or param_plot_extension == 'svg'</filter> 202 <filter>not param_collection and (param_plot_extension == 'png' or param_plot_extension == 'svg')</filter>
193 </data> 203 </data>
194 <collection name="images" type="list" label="${tool.name} on ${on_string}: images"> 204 <collection name="images" type="list" label="${tool.name} on ${on_string}: images">
195 <filter>param_plot_extension == 'pdf'</filter> 205 <filter>param_collection or param_plot_extension == 'pdf'</filter>
196 <discover_datasets pattern="__name_and_ext__" directory="images" /> 206 <discover_datasets pattern="__name_and_ext__" directory="images" />
197 </collection> 207 </collection>
198 </outputs> 208 </outputs>
199 <tests> 209 <tests>
200 <test> 210 <test>
201 <param name="param_in_mzML" value="MetaProSIP_1_input.mzML"/> 211 <param name="param_in_mzML" value="MetaProSIP_1_input.mzML" ftype="mzml"/>
202 <param name="param_in_fasta" value="MetaProSIP_1_input.fasta"/> 212 <param name="param_in_fasta" value="MetaProSIP_1_input.fasta" ftype="fasta"/>
203 <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML"/> 213 <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML" ftype="featurexml"/>
204 <output name="param_out_csv" file="MetaProSIP_1_output_1.csv" /> 214 <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" /> 215 <output name="param_out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" lines_diff="2"/>
206 </test> 216 </test>
207 </tests> 217 </tests>
208 <help>Performs proteinSIP on peptide features for elemental flux analysis. 218 <help>Performs proteinSIP on peptide features for elemental flux analysis.
209 219
210 220 ** Galaxy specific notes **
211 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html</help> 221
222 The peptide centric tabular data set generated by the tool is not rendered properly by Galaxy, because it has more than 50 columns. You might extract columns of interst.
223 </help>
212 <expand macro="references"/> 224 <expand macro="references"/>
213 </tool> 225 </tool>