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annotate pepquery.xml @ 0:32d3818fc635 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
author galaxyp
date Wed, 22 Jan 2020 17:12:37 -0500
parents
children 528bcf03e561
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32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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1 <tool id="pepquery" name="PepQuery" version="@VERSION@.0">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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3 <macros>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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4 <import>macros.xml</import>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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5 </macros>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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6 <requirements>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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7 <requirement type="package" version="@VERSION@">pepquery</requirement>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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8 </requirements>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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9 <stdio>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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10 <exit_code range="1:" level="fatal" description="Failed" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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11 <regex match="Exception"
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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12 source="stderr"
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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13 level="fatal"
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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14 description="java Exception" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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15 </stdio>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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16 <command><![CDATA[
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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17 #import re
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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18 #set $spectrum_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.spectrum_file.display_name.split('/')[-1])) + ".mgf"
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_file.display_name.split('/')[-1])) + ".fa"
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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20 ln -s '$req_inputs.spectrum_file' '$spectrum_file' &&
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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21 ln -s '$req_inputs.db_file' '$db_file' &&
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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22 pepquery
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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23 -ms '$spectrum_file'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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24 -db '$db_file'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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25 #if $req_inputs.input_type.input_type_selector == 'peptide'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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26 -pep '$req_inputs.input_type.multiple.input'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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27 #else
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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28 -t '$req_inputs.input_type.input_type_selector'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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29 #if int(str($req_inputs.input_type.input_type_selector)) == 1
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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30 -i '$req_inputs.input_type.multiple.input'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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31 #else
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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32 -i '$req_inputs.input_type.input'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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33 #if int(str($req_inputs.input_type.input_type_selector)) == 2
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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34 #if $req_inputs.input_type.frame == 'None'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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35 -f '0'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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36 #else
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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37 -f '$req_inputs.input_type.frame'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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38 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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39 #else
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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40 -anno '$req_inputs.input_type.anno'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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41 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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42 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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43 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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44 #if $modifications.fixed_mod
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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45 -fixMod '$modifications.fixed_mod'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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46 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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47 #if $modifications.var_mod
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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48 -varMod '$modifications.var_mod'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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49 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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50 -maxVar '$modifications.max_mods'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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51 $modifications.unmodified
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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52 $modifications.aa
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53 -tol '$ms_params.tolerance_params.precursor_tolerance'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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54 -tolu '$ms_params.tolerance_params.precursor_unit'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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55 -itol '$ms_params.tolerance_params.tolerance'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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56 -e '$ms_params.digestion.enzyme'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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57 -fragmentMethod '$ms_params.search.frag_method'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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58 -m '$ms_params.search.scoring_method'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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59 -maxCharge '$ms_params.search.max_charge'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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60 -minCharge '$ms_params.search.min_charge'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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61 -minPeaks '$ms_params.search.min_peaks'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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62 -minScore '$ms_params.search.min_score'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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63 -maxLength '$ms_params.search.max_length'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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64 -n '$ms_params.search.num_random_peptides'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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65 -o pepquery_output
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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66 | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2)
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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67 #if $report_spectrum_file:
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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68 && for f in pepquery_output/psm.txt pepquery_output/psm_annotation.txt pepquery_output/detail.txt pepquery_output/psm_rank.txt; do if [ -e \${f} ]; then cp \${f} \${f}.orig; awk 'BEGIN{FS="\t"; OFS="\t"; stc = 0;}; NR==1{for (i = 1; i <= NF; i++) {if (\$i == "spectrum_title") stc = i;}}; NR==1{if (stc>0){\$stc = "spectrum_file" FS \$stc}; print}; NR>1{if (stc>0){\$stc = "$spectrum_file" FS \$stc}; print}' \${f}.orig > \${f};fi;done
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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69 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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70 ]]>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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71 </command>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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72 <inputs>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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73 <section name="req_inputs" title="Input Data" expanded="true">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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74 <conditional name="input_type">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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75 <param name="input_type_selector" type="select" label="Input Type" argument="-t" help="" >
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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76 <option value="peptide">peptide</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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77 <option value="1">protein</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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78 <option value="2">DNA (translate to protein sequences)</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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79 <!-- these are not working with pepquery version 1.3
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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80 <option value="3">VCF (translate to protein sequences)</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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81 <option value="4">BED (translate to protein sequences)</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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82 <option value="5">GTF (translate to protein sequences)</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
83 -->
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
84 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
85 <when value="peptide">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
86 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
87 <param name="peptide_input_selector" type="select" label="Peptides?">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
88 <option value="multiple">Peptide list from your history</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
89 <option value="single">Single peptide entered as text</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
90 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
91 <when value="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
92 <param name="input" type="data" format="txt" label="Peptide Sequences (.txt)" argument="-pep" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
93 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
94 <when value="single">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
95 <param name="input" type="text" label="Peptide Sequence" argument="-pep" help="Peptide sequence which you want to search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
96 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
97 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
98 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
99 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
100 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
101 <when value="1">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
102 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
103 <param name="protein_input_selector" type="select" label="Proteins?">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
104 <option value="multiple">Protein fasta from your history</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
105 <option value="single">Single protein entered as text</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
106 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
107 <when value="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
108 <param name="input" type="data" format="fasta" label="Protein Sequences (.txt)" argument="-i" help="Protein fasta file containing proteins which you want to search." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
109 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
110 <when value="single">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
111 <param name="input" type="text" label="Protein Sequence" argument="-i" help="Protein sequence which you want to search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
112 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
113 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
114 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
115 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
116 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
117 <when value="2">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
118 <param name="input" type="text" label="DNA Sequence (at least 60 bp)" argument="-i" help="DNA sequence which you want to search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
119 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
120 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
121 <param name="frame" type="select" label="Frame(s) for DNA translation" argument="-f" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
122 <option value="1">1</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
123 <option value="2">2</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
124 <option value="3">3</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
125 <option value="4">4</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
126 <option value="5">5</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
127 <option value="6">6</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
128 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
129 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
130 <!-- these are not working with pepquery version 1.3
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
131 <when value="3">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
132 <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
133 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
134 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
135 <when value="4">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
136 <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
137 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
138 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
139 <when value="5">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
140 <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
141 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
142 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
143 -->
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
144 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
145 <param name="db_file" type="data" format="fasta" label="Protein Reference Database File" argument="-db" help="an input sequence that matches a reference will be ignored." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
146 <param name="spectrum_file" type="data" format="mgf" label="Spectrum File" argument="-ms" help="Spectrum file used for identification, mgf format" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
147 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
148 <section name="modifications" title="Modifications" expanded="false">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
149 <param name="fixed_mod" type="select" label="Fixed modification(s)" multiple="true" argument="-fixMod" help="Fixed modification">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
150 <option value="6" selected="true">Carbamidomethylation of C (57.02146372057) modaa</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
151 <option value="117">Oxidation of M (15.99491461956) modaa</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
152 <expand macro="modifications" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
153 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
154 <param name="var_mod" type="select" label="Variable modification(s)" multiple="true" argument="-varMod" help="Variable modification" >
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
155 <option value="117" selected="true">Oxidation of M (15.99491461956) modaa</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
156 <option value="6">Carbamidomethylation of C (57.02146372057) modaa</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
157 <expand macro="modifications" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
158 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
159 <param name="max_mods" type="integer" label="Max Modifications" value="3" argument="-maxVar" help="Max number of variable modifications" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
160 <param name="unmodified" type="boolean" truevalue="-um" falsevalue="" checked="false" label="Unmodified?" argument="-um" help="Validation with unrestricted modification searching" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
161 <param name="aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" argument="-aa" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
162 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
163 <section name="ms_params" title="Mass spectrometer" expanded="false">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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164 <section name="tolerance_params" title="Tolerance" expanded="true">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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165 <param name="precursor_tolerance" type="integer" value="10" label="Precursor Tolerance" argument="-tol" help="the error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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166 <param name="precursor_unit" type="select" label="Precursor Unit" argument="-tolu" help="The unit of precursor ion m/z tolerance">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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167 <option value="ppm" selected="true">ppm</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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168 <option value="Da">Da</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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169 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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170 <param name="tolerance" type="float" value="0.6" label="Tolerance" argument="-itol" help="Error window for MS/MS fragment ion mass values in Da unit." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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171 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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172 <section name="digestion" title="Digestion" expanded="false">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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173 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="Enzyme used for protein digestion" >
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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174 <option value="0">Non enzyme</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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175 <option value="1" selected="true">Trypsin</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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176 <option value="2">Trypsin (no P rule)</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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177 <option value="3">Arg-C</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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178 <option value="4">Arg-C (no P rule)</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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179 <option value="5">Arg-N</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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180 <option value="6">Glu-C</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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181 <option value="7">Lys-C</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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182 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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183 <param name="max_missed_cleavages" type="integer" value="2" label="Max Missed Cleavages" argument="-c" help="The max missed cleavages" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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184 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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185 <section name="search" title="PSM" expanded="false">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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186 <param name="frag_method" type="select" label="Fragmentation Method" argument="-fragmentMethod">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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187 <option value="1" selected="true">CID/HCD</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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188 <option value="2">ETD</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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189 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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190 <param name="scoring_method" type="select" label="Scoring Method" argument="-m">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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191 <option value="1" selected="true">HyperScore</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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192 <option value="2">MVH</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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193 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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194 <param name="max_charge" type="integer" value="3" label="Max Charge" argument="-maxCharge" help="The maximum charge to consider if the charge state is not available" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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195 <param name="min_charge" type="integer" value="2" label="Minimum Charge" argument="-minCharge" help="The minimum charge to consider if the charge state is not available" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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196 <param name="min_peaks" type="integer" value="10" label="Minimum Peaks" argument="-minPeaks" help="Min peaks in spectrum" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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197 <param name="min_score" type="integer" value="12" label="Minimum Score" argument="-minScore" help="Minimum score to consider for peptide searching" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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198 <param name="max_length" type="integer" value="45" label="Maximum length of peptide" argument="-maxLength" help="The maximum length of peptide to consider." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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199 <param name="num_random_peptides" type="integer" value="1000" label="Number of Random Peptides" argument="-n" help="The number of random peptides" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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200 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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201 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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202 <param name="report_spectrum_file" type="boolean" truevalue="spectrum_file," falsevalue="" checked="false" label="Add spectrum_file column" help="Add a spectrum_file column before the spectrum_title column. Useful for combining pepquery outputs." />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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203 </inputs>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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204 <outputs>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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205 <data format="tabular" name="psm_annotation" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: PSM Annotation">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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206 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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207 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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208 <action name="column_names" type="metadata" default="peptide,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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209 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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210 </data>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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211 <data format="tabular" name="detail" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: Detail">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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212 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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213 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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214 <action name="column_names" type="metadata" default="${report_spectrum_file}spectrum_title,peptide,modification,pep_mass,score" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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215 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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216 </data>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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217 <data format="tabular" name="psm" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: PSM">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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218 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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219 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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220 <action name="column_names" type="metadata" default="peptide,modification,n,${report_spectrum_file}spectrum_title,charge,exp_mass,ppm,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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221 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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222 </data>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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223 <data format="tabular" name="psm_rank_txt" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: PSM Rank (txt)">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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224 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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225 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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226 <action name="column_names" type="metadata" default="peptide,modification,n,${report_spectrum_file}spectrum_title,charge,exp_mass,ppm,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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227 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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228 </data>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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229 <data format="mgf" name="psm_rank_mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: PSM Rank (mgf)"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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230 </outputs>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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231 <tests>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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232 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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233 <section name="req_inputs">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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234 <conditional name="input_type">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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235 <param name="input_type_selector" value="peptide"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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236 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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237 <param name="peptide_input_selector" value="single" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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238 <param name="input" value="ELGSSDLTAR"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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239 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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240 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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241 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
242 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
243 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
244 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
245 <param name="fixed_mod" value="6,103,157"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
246 <param name="var_mod" value="117"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
247 <param name="max_mods" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
248 <param name="unmodified" value="False"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
249 <param name="aa" value="True"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
250 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
251 <section name="ms_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
252 <section name="tolerance_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
253 <param name="precursor_tolerance" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
254 <param name="precursor_unit" value="ppm"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
255 <param name="tolerance" value="0.6"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
256 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
257 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
258 <param name="enzyme" value="0"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
259 <param name="max_missed_cleavages" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
260 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
261 <section name="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
262 <param name="frag_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
263 <param name="scoring_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
264 <param name="max_charge" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
265 <param name="min_charge" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
266 <param name="min_peaks" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
267 <param name="min_score" value="12"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
268 <param name="max_length" value="45"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
269 <param name="num_random_peptides" value="1000"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
270 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
271 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
272 <param name="report_spectrum_file" value="true"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
273 <output name="psm_rank_txt">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
274 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
275 <has_text text="ELGSSDLTAR" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
276 </assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
277 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
278 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
279
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
280 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
281 <section name="req_inputs">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
282 <conditional name="input_type">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
283 <param name="input_type_selector" value="peptide"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
284 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
285 <param name="peptide_input_selector" value="multiple" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
286 <param name="input" ftype="tabular" value="novel_peptides"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
287 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
288 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
289 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
290 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
291 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
292 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
293 <param name="fixed_mod" value="6,103,157"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
294 <param name="var_mod" value="117"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
295 <param name="max_mods" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
296 <param name="unmodified" value="False"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
297 <param name="aa" value="True"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
298 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
299 <section name="ms_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
300 <section name="tolerance_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
301 <param name="precursor_tolerance" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
302 <param name="precursor_unit" value="ppm"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
303 <param name="tolerance" value="0.6"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
304 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
305 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
306 <param name="enzyme" value="0"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
307 <param name="max_missed_cleavages" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
308 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
309 <section name="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
310 <param name="frag_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
311 <param name="scoring_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
312 <param name="max_charge" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
313 <param name="min_charge" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
314 <param name="min_peaks" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
315 <param name="min_score" value="12"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
316 <param name="max_length" value="45"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
317 <param name="num_random_peptides" value="1000"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
318 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
319 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
320 <param name="report_spectrum_file" value="true"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
321 <output name="psm_rank_txt">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
322 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
323 <has_text text="ELGSSDLTAR" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
324 <has_text text="SPYREFTDHLVK" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
325 </assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
326 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
327 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
328
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
329 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
330 <section name="req_inputs">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
331 <conditional name="input_type">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
332 <param name="input_type_selector" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
333 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
334 <param name="protein_input_selector" value="multiple" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
335 <param name="input" ftype="fasta" value="novel_proteins.fa"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
336 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
337 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
338 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
339 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
340 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
341 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
342 <param name="fixed_mod" value="6,103,157"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
343 <param name="var_mod" value="117"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
344 <param name="max_mods" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
345 <param name="unmodified" value="False"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
346 <param name="aa" value="True"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
347 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
348 <section name="ms_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
349 <section name="tolerance_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
350 <param name="precursor_tolerance" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
351 <param name="precursor_unit" value="ppm"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
352 <param name="tolerance" value="0.6"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
353 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
354 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
355 <param name="enzyme" value="0"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
356 <param name="max_missed_cleavages" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
357 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
358 <section name="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
359 <param name="frag_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
360 <param name="scoring_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
361 <param name="max_charge" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
362 <param name="min_charge" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
363 <param name="min_peaks" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
364 <param name="min_score" value="12"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
365 <param name="max_length" value="45"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
366 <param name="num_random_peptides" value="1000"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
367 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
368 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
369 <param name="report_spectrum_file" value="true"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
370 <output name="psm_rank_txt">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
371 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
372 <has_text text="ELGSSDLTAR" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
373 <has_text text="SPYREFTDHLVK" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
374 </assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
375 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
376 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
377
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
378 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
379 <section name="req_inputs">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
380 <conditional name="input_type">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
381 <param name="input_type_selector" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
382 <param name="input" value="gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
383 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
384 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
385 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
386 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
387 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
388 <param name="fixed_mod" value="6,103,157"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
389 <param name="var_mod" value="117"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
390 <param name="max_mods" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
391 <param name="unmodified" value="False"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
392 <param name="aa" value="True"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
393 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
394 <section name="ms_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
395 <section name="tolerance_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
396 <param name="precursor_tolerance" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
397 <param name="precursor_unit" value="ppm"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
398 <param name="tolerance" value="0.6"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
399 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
400 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
401 <param name="enzyme" value="0"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
402 <param name="max_missed_cleavages" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
403 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
404 <section name="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
405 <param name="frag_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
406 <param name="scoring_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
407 <param name="max_charge" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
408 <param name="min_charge" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
409 <param name="min_peaks" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
410 <param name="min_score" value="12"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
411 <param name="max_length" value="45"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
412 <param name="num_random_peptides" value="1000"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
413 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
414 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
415 <param name="report_spectrum_file" value="true"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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416 <output name="psm_rank_txt">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
417 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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418 <has_text text="ELGSSDLTAR" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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419 </assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
420 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
421 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
422
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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423 </tests>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
424 <help><![CDATA[
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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425 PepQuery is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
426
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
427 **Inputs**
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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428 - A sequence to match, one of the following:
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
429
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
430 - A peptide string or a history dataset with a list of peptides
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
431 - A protein string or a history dataset with a protein fasta
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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432 - A DNA string that is at least 60 base pairs in length
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
433
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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434 - A mass spectrometry MGF file
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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435 - A reference protein fasta database, peptides matching a reference sequence will be excluded.
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
436
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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437 **Outputs**
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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438 - PSM annotation - tabular with columns:
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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439 peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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440 - Detail - tabular with columns:
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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441 *report_spectrum_file* spectrum_title peptide modification pep_mass score
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
442 - PSM - tabular with columns:
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
443 peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
444 - PSM Rank - tabular with columns:
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
445 peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm*
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
446 - An MGF with the best matching spectrums
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
447
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
448 The *report_spectrum_file* is an optional field that can be added.
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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449 The *n_ptm* field is added when using unrestricted modification searching (-um).
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
450
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
451
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
452 ]]></help>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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diff changeset
453 <citations>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
454 <citation type="doi">10.1101/gr.235028.118</citation>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
455 </citations>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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diff changeset
456 </tool>