Mercurial > repos > galaxyp > openms_metaprosip

comparison MetaProSIP.xml @ 13:3a2985428366 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 05:13:44 -0400
parents d06e5c4396d7
children 7a0f18ee26c9
comparison
equal deleted inserted replaced
12:b57027b6a56c 13:3a2985428366
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 CTD2Galaxy.--> 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="2.2.0.1"> 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="references"/> 10 <expand macro="requirements">
11 <requirement type="package" version="3.4.1">r-base</requirement>
12 <requirement type="package" version="3.0.1">r-gplots</requirement>
13 </expand>
11 <expand macro="stdio"/> 14 <expand macro="stdio"/>
12 <expand macro="requirements"> 15 <command detect_errors="aggressive"><![CDATA[
13 <requirement type="package" version="3.3.1">r-base</requirement> 16 MetaProSIP
14 </expand>
15 <command>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:
22 #end if 23 #end if
23 #if $param_out_csv: 24 #if $param_out_csv:
24 -out_csv $param_out_csv 25 -out_csv $param_out_csv
25 #end if 26 #end if
26 #if $param_out_peptide_centric_csv: 27 #if $param_out_peptide_centric_csv:
27 -out_peptide_centric_csv $param_out_peptide_centric_csv 28 -out_peptide_centric_csv param_out_peptide_centric_csv
28 #end if 29 #end if
29 #if $param_in_featureXML: 30 #if $param_in_featureXML:
30 -in_featureXML $param_in_featureXML 31 -in_featureXML $param_in_featureXML
31 #end if 32 #end if
32
33 -r_executable 'R'
34
35 #if $param_mz_tolerance_ppm: 33 #if $param_mz_tolerance_ppm:
36 -mz_tolerance_ppm $param_mz_tolerance_ppm 34 -mz_tolerance_ppm $param_mz_tolerance_ppm
37 #end if 35 #end if
38 #if $param_rt_tolerance_s: 36 #if $param_rt_tolerance_s:
39 -rt_tolerance_s $param_rt_tolerance_s 37 -rt_tolerance_s $param_rt_tolerance_s
59 "$param_plot_extension" 57 "$param_plot_extension"
60 #else 58 #else
61 $param_plot_extension 59 $param_plot_extension
62 #end if 60 #end if
63 #end if 61 #end if
64 #if $param_qc_output_directory: 62 -qc_output_directory images
65 -qc_output_directory "$param_qc_output_directory"
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
128 #end if 124 #end if
129 #if $adv_opts.param_force: 125 #if $adv_opts.param_force:
130 -force 126 -force
131 #end if 127 #end if
132 #end if 128 #end if
133 </command> 129 -threads "\${GALAXY_SLOTS:-1}"
130
131 ## - add comment char to first line,
132 ## - remove leading/trailing spaces in fields
133 ## - remove empty line(s)
134 ## - remove 'file://' and get basename of filenames in the table
135 ## - add empty fields as '0' (MetaproSIP output has varying number of output columns, ie it omits the last columns if there are no values)
136 && cat param_out_peptide_centric_csv |
137 sed '1 s/^/#/' |
138 sed 's/\t /\t/g; s/ \t/\t/g; s/ /_/g' |
139 grep -v "^$" |
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"
142
143 ## get html file (should be only one [?])
144
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}'
150 #end if
151 ]]></command>
134 <inputs> 152 <inputs>
135 <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) "/>
136 <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) "/>
137 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/> 155 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
138 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/> 156 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
139 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/> 157 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
140 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/> 158 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
141 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/> 159 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
142 <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/> 160 <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
143 <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/> 161 <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R² of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
144 <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) "/> 162 <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) "/>
145 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) "> 163 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
146 <option value="png" selected="true">png</option> 164 <option value="png" selected="true">png</option>
147 <option value="svg">svg</option> 165 <option value="svg">svg</option>
148 <option value="pdf">pdf</option> 166 <option value="pdf">pdf</option>
149 </param>
150 <param name="param_qc_output_directory" type="text" size="30" label="Output directory for the quality report" help="(-qc_output_directory) ">
151 <sanitizer>
152 <valid initial="string.printable">
153 <remove value="'"/>
154 <remove value="&quot;"/>
155 </valid>
156 </sanitizer>
157 </param> 167 </param>
158 <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) "> 168 <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 <option value="C" selected="true">C</option> 169 <option value="C" selected="true">C</option>
160 <option value="N">N</option> 170 <option value="N">N</option>
161 <option value="H">H</option> 171 <option value="H">H</option>
164 <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) "/>
165 <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) "/>
166 <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) "/>
167 <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) "/>
168 <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)"/>
169 <expand macro="advanced_options"> 180 <expand macro="advanced_options">
170 <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"/>
171 <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) "/>
172 <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) "/>
173 <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) "/>
183 <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"/> 194 <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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 195 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
185 </expand> 196 </expand>
186 </inputs> 197 </inputs>
187 <outputs> 198 <outputs>
188 <data name="param_out_csv" format="tabular"/> 199 <data name="param_out_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/>
189 <data name="param_out_peptide_centric_csv" format="tabular"/> 200 <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/>
201 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage">
202 <filter>not param_collection and (param_plot_extension == 'png' or param_plot_extension == 'svg')</filter>
203 </data>
204 <collection name="images" type="list" label="${tool.name} on ${on_string}: images">
205 <filter>param_collection or param_plot_extension == 'pdf'</filter>
206 <discover_datasets pattern="__name_and_ext__" directory="images" />
207 </collection>
190 </outputs> 208 </outputs>
209 <tests>
210 <test>
211 <param name="param_in_mzML" value="MetaProSIP_1_input.mzML" ftype="mzml"/>
212 <param name="param_in_fasta" value="MetaProSIP_1_input.fasta" ftype="fasta"/>
213 <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML" ftype="featurexml"/>
214 <output name="param_out_csv" file="MetaProSIP_1_output_1.csv"/>
215 <output name="param_out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" lines_diff="2"/>
216 </test>
217 </tests>
191 <help>Performs proteinSIP on peptide features for elemental flux analysis. 218 <help>Performs proteinSIP on peptide features for elemental flux analysis.
192 219
193 220 ** Galaxy specific notes **
194 For more information, visit http://www.openms.de/comp/metaprosip/</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>
224 <expand macro="references"/>
195 </tool> 225 </tool>