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comparison metanovo.xml @ 4:7a5ff5359b13 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8"
author galaxyp
date Fri, 22 Apr 2022 13:31:08 +0000
parents 4a851c02f558
children d6dcd3173bdf
comparison
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3:4a851c02f558 4:7a5ff5359b13
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
7 </requirements> 7 </requirements>
8 <macros> 8 <macros>
9 <token name="@TOOL_VERSION@">1.9.4</token> 9 <token name="@TOOL_VERSION@">1.9.4</token>
10 <token name="@VERSION_SUFFIX@">3</token> 10 <token name="@VERSION_SUFFIX@">4</token>
11 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token> 11 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token>
12 <import>macros_modifications.xml</import> 12 <import>macros_modifications.xml</import>
13 </macros> 13 </macros>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
29 #else 29 #else
30 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_type.input_mgf.element_identifier)) 30 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_type.input_mgf.element_identifier))
31 ln -s '$input_type.input_mgf' '$mgf_dir/$mgf_name' && 31 ln -s '$input_type.input_mgf' '$mgf_dir/$mgf_name' &&
32 #end if 32 #end if
33 33
34 cat $metanovo_config > config.sh && 34 ## the number of threads should be number of available threads-1 according to the docs
35 threads=\${GALAXY_SLOTS:-3} &&
36 if [ \$threads -gt 1 ]; then
37 (( threads-- ));
38 fi &&
39 echo "THREAD_LIMIT=\$threads" >> config.sh &&
40
35 metanovo.sh config.sh 41 metanovo.sh config.sh
36 ]]> 42 ]]>
37 </command> 43 </command>
38 44
39 <configfiles> 45 <configfiles>
40 <configfile name="metanovo_config"><![CDATA[#slurp 46 <configfile filename="config.sh"><![CDATA[#slurp
41 #import re 47 #import re
42 MGF_FOLDER=mgf_files 48 MGF_FOLDER=mgf_files
43 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_fasta.element_identifier)) 49 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_fasta.element_identifier))
44 FASTA_FILE=fasta_file/'$fasta_name' 50 FASTA_FILE=fasta_file/'$fasta_name'
45 OUTPUT_FOLDER=. 51 OUTPUT_FOLDER=.
46 CHUNKSIZE=$processing_control.CHUNKSIZE 52 CHUNKSIZE=$processing_control.CHUNKSIZE
47 THREAD_LIMIT=$processing_control.THREAD_LIMIT 53 JVM_Xmx='10000M'
48 JVM_Xmx='$processing_control.JVM_Xmx' 54 JVM_Xms='1024M'
49 JVM_Xms='$processing_control.JVM_Xms'
50 mn_specificity='$metanovo_parameters.mn_specificity' 55 mn_specificity='$metanovo_parameters.mn_specificity'
51 mn_enzymes='$metanovo_parameters.mn_enzymes' 56 mn_enzymes='$metanovo_parameters.mn_enzymes'
52 mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages 57 mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages
53 dg_pepnovo=0 58 dg_pepnovo=0
54 dg_pnovo=0 59 dg_pnovo=0
143 148
144 <param name="input_fasta" type="data" format="fasta" label="FASTA File" /> 149 <param name="input_fasta" type="data" format="fasta" label="FASTA File" />
145 150
146 <section name="processing_control" expanded="False" title="Processing Control"> 151 <section name="processing_control" expanded="False" title="Processing Control">
147 <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/> 152 <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/>
148 <param name="THREAD_LIMIT" label="How many threads to use per node" value="2" type="integer" optional="true"/>
149 <param name="JVM_Xmx" label="Maximum memory allocated to each Java thread" value="10000M" type="text" optional="true"/>
150 <param name="JVM_Xms" label="Minimum memory allocated to each Java thread" value="1024M" type="text" optional="true"/>
151 </section> 153 </section>
152 <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters"> 154 <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">
153 <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select"> 155 <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select">
154 <option selected="true" value="specific">specific</option> 156 <option selected="true" value="specific">specific</option>
155 <option value="semi-specific">semi-specific</option> 157 <option value="semi-specific">semi-specific</option>
300 <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/> 302 <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
301 <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/> 303 <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
302 </section> 304 </section>
303 </inputs> 305 </inputs>
304 <outputs> 306 <outputs>
305 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="MetaNovo Output FASTA"/> 307 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="${tool.name} on ${on_string}: FASTA"/>
306 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="MetaNovo Output CSV"/> 308 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="${tool.name} on ${on_string}: CSV"/>
307 </outputs> 309 </outputs>
310 <tests>
311 <test expect_num_outputs="2">
312 <param name="input_mgf" value="sample_data_1.mgf" ftype="mgf"/>
313 <param name="input_fasta" value="sample_fasta_single.fasta" ftype="fasta"/>
314 <output name="output_csv" ftype="csv">
315 <assert_contents>
316 <!-- Check header. -->
317 <has_text text=",index,Accession,Record,ID,PeptideCount,Peptides,ScanCount,Scans,Organism,Length,File,Sample sample_data_1 (msms),SAF sample_data_1,NSAF sample_data_1,Summed_NSAF,Protein_Prob,Organism_Prob,MSMS_Percent,Combined_Prob"/>
318 </assert_contents>
319 </output>
320 <output name="output_fasta" ftype="fasta" file="sample_output_single.fasta"/>
321 </test>
322 <test expect_num_outputs="2">
323 <param name="type" value="collection"/>
324 <param name="input_mgf_collection">
325 <collection type="list">
326 <element name="sample_data_1.mgf" value="sample_data_1.mgf" />
327 <element name="sample_data_2.mgf" value="sample_data_2.mgf" />
328 </collection>
329 </param>
330 <param name="input_fasta" value="sample_fasta_collection.fasta" ftype="fasta"/>
331 <output name="output_csv" ftype="csv">
332 <assert_contents>
333 <!-- Check header. -->
334 <has_text text=",index,Accession,File,ID,Length,Organism,PeptideCount,Peptides,Record,SAF sample_data_1,SAF sample_data_2,Sample sample_data_1 (msms),Sample sample_data_2 (msms),ScanCount,Scans,NSAF sample_data_1,NSAF sample_data_2,Summed_NSAF,Protein_Prob,Organism_Prob,MSMS_Percent,Combined_Prob"/>
335 </assert_contents>
336 </output>
337 <output name="output_fasta" ftype="fasta" file="sample_output_collection.fasta"/>
338 </test>
339 </tests>
308 <help><![CDATA[ 340 <help><![CDATA[
309 **MetaNovo** 341 **MetaNovo**
310 342
311 MetaNovo searches MS/MS data against a FASTA database of known proteins. 343 MetaNovo searches MS/MS data against a FASTA database of known proteins.
312 344