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annotate pepquery.xml @ 2:5b5a9f59e2c7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
author galaxyp
date Mon, 15 Mar 2021 12:52:03 +0000
parents 528bcf03e561
children
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2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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1 <tool id="pepquery" name="PepQuery" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
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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>
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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>
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6 <requirements>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
0
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Failed" />
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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"
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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>
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16 <command><![CDATA[
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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' &&
2
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22 #if $req_inputs.tags.tagType == 'pFind':
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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23 pepquery main.java.util.generateTags '$req_inputs.tags.qry_res' > qry.tags &&
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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24 #end if
0
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25 pepquery
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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26 -ms '$spectrum_file'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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27 -db '$db_file'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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28 #if $req_inputs.input_type.input_type_selector == 'peptide'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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29 -pep '$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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30 #else
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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31 -t '$req_inputs.input_type.input_type_selector'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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32 #if int(str($req_inputs.input_type.input_type_selector)) == 1
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33 -i '$req_inputs.input_type.multiple.input'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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34 #else
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35 -i '$req_inputs.input_type.input'
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36 #if int(str($req_inputs.input_type.input_type_selector)) == 2
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37 #if $req_inputs.input_type.frame == 'None'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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38 -f '0'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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39 #else
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40 -f '$req_inputs.input_type.frame'
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41 #end if
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42 #else
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43 -anno '$req_inputs.input_type.anno'
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44 #end if
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45 #end if
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46 #end if
1
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47 -indexType $req_inputs.indexType
2
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48 #if $req_inputs.tags.tagType == 'PepQuery':
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49 -tag '$req_inputs.tags.tag_file'
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50 -tagIndexType $req_inputs.tags.tagIndexType
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51 #elif $req_inputs.tags.tagType == 'pFind':
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52 -tag qry.tags
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53 -tagIndexType 2
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54 #end if
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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55 #if $modifications.fixed_mod
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56 -fixMod '$modifications.fixed_mod'
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57 #end if
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58 #if $modifications.var_mod
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59 -varMod '$modifications.var_mod'
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60 #end if
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61 -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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62 $modifications.unmodified
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63 $modifications.aa
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64 -tol '$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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65 -tolu '$ms_params.tolerance_params.precursor_unit'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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66 -itol '$ms_params.tolerance_params.tolerance'
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67 -e '$ms_params.digestion.enzyme'
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68 -fragmentMethod '$ms_params.search.frag_method'
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69 -m '$ms_params.search.scoring_method'
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70 -maxCharge '$ms_params.search.max_charge'
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71 -minCharge '$ms_params.search.min_charge'
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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72 -minPeaks '$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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73 -minScore '$ms_params.search.min_score'
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74 -maxLength '$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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75 -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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76 -o pepquery_output
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77 | 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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78 #if $report_spectrum_file:
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79 && for f in pepquery_output/psm.txt pepquery_output/psm_annotation.txt pepquery_output/detail.txt pepquery_output/psm_rank.txt; do if [ -e \${f} ]; then cp \${f} \${f}.orig; awk 'BEGIN{FS="\t"; OFS="\t"; stc = 0;}; NR==1{for (i = 1; i <= NF; i++) {if (\$i == "spectrum_title") stc = i;}}; NR==1{if (stc>0){\$stc = "spectrum_file" FS \$stc}; print}; NR>1{if (stc>0){\$stc = "$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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80 #end if
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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81 ]]>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
82 </command>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
83 <inputs>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
84 <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"
galaxyp
parents:
diff changeset
85 <conditional name="input_type">
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
86 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
87 <option value="peptide">peptide</option>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
88 <option value="1">protein</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="2">DNA (translate to protein sequences)</option>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
90 <!-- these are not working with pepquery version 1.6
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
91 <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"
galaxyp
parents:
diff changeset
92 <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"
galaxyp
parents:
diff changeset
93 <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
94 -->
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
95 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
96 <when value="peptide">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
97 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
98 <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
99 <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
100 <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
101 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
102 <when value="multiple">
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
103 <param name="input" argument="-pep" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
104 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
105 <when value="single">
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
106 <param name="input" argument="-pep" type="text" label="Peptide Sequence" help="Peptide sequence which you want to search">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
107 <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
108 </param>
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 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
111 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
112 <when value="1">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
113 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
114 <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
115 <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
116 <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
117 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
118 <when value="multiple">
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
119 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
120 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
121 <when value="single">
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
122 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
123 <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
124 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
125 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
126 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
127 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
128 <when value="2">
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
129 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
130 <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
131 </param>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
132 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
133 <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
134 <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
135 <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
136 <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
137 <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
138 <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
139 </param>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
140 </when>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
141 <!-- these are not working with pepquery version 1.6
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
142 <when value="3">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
143 <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
144 <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
145 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
146 <when value="4">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
147 <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
148 <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
149 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
150 <when value="5">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
151 <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
152 <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
153 </when>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
154 -->
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
155 </conditional>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
156 <param name="db_file" argument="-db" type="data" format="fasta" label="Protein Reference Database File" help="an input sequence that matches a reference will be ignored." />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
157 <param name="spectrum_file" argument="-ms" type="data" format="mgf" label="Spectrum File" help="Spectrum file used for identification, mgf format" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
158 <param name="indexType" argument="-indexType" type="select" label="Report Spectrum Scan as" help="" >
1
528bcf03e561 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
159 <option value="1" selected="true">index (1-based) in MGF</option>
528bcf03e561 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
160 <option value="2">spectrum title in MGF</option>
528bcf03e561 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
161 </param>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
162 <conditional name="tags">
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163 <param name="tagType" type="select" label="Tag File">
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164 <option value="None">None</option>
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165 <option value="PepQuery">PepQuery</option>
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166 <option value="pFind">pFind</option>
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167 </param>
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168 <when value="None"/>
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169 <when value="PepQuery">
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170 <param name="tag_file" argument="-tag" type="data" format="txt" label="PepPuery Tag File"/>
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171 <param name="tagIndexType" argument="-tagIndexType" type="select" label="Tag File Index Type" help="pFind uses the spectrum title" >
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172 <option value="1">index (1-based) in MGF</option>
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173 <option value="2" selected="true">spectrum title in MGF</option>
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174 </param>
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175 </when>
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176 <when value="pFind">
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177 <param name="qry_res" type="data" format="txt" label="pFind .qry.res" help="pFind can be used to generate a tags file for no-enzyme immunopeptidomics search" />
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178 </when>
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179 </conditional>
0
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180 </section>
2
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181
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182 <!--
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183 <section name="tags" title="Tags File" expanded="false">
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184 <param name="qry_res" type="data" format="txt" optional="true" label="pFind .qry.res" help="pFind can be used to generate a tags file for no-enzyme immunopeptidomics search" />
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185 </section>
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186 -->
0
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187 <section name="modifications" title="Modifications" expanded="false">
2
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188 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" help="Fixed modification">
0
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189 <option value="6" selected="true">Carbamidomethylation of C (57.02146372057) modaa</option>
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190 <option value="117">Oxidation of M (15.99491461956) modaa</option>
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191 <expand macro="modifications" />
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192 </param>
2
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193 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" help="Variable modification" >
0
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194 <option value="117" selected="true">Oxidation of M (15.99491461956) modaa</option>
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195 <option value="6">Carbamidomethylation of C (57.02146372057) modaa</option>
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196 <expand macro="modifications" />
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197 </param>
2
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198 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="3" help="Max number of variable modifications" />
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199 <param name="unmodified" argument="-um" type="boolean" truevalue="-um" falsevalue="" checked="false" label="Unmodified?" help="Validation with unrestricted modification searching" />
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200 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
0
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201 </section>
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202 <section name="ms_params" title="Mass spectrometer" expanded="false">
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203 <section name="tolerance_params" title="Tolerance" expanded="true">
2
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204 <param name="precursor_tolerance" argument="-tol" type="integer" value="10" label="Precursor Tolerance" 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." />
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205 <param name="precursor_unit" argument="-tolu" type="select" label="Precursor Unit" help="The unit of precursor ion m/z tolerance">
0
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206 <option value="ppm" selected="true">ppm</option>
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207 <option value="Da">Da</option>
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208 </param>
2
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209 <param name="tolerance" argument="-itol" type="float" value="0.6" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit." />
0
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210 </section>
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211 <section name="digestion" title="Digestion" expanded="false">
2
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212 <param name="enzyme" argument="-e" type="select" label="Enzyme" help="Enzyme used for protein digestion" >
0
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213 <option value="0">Non enzyme</option>
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214 <option value="1" selected="true">Trypsin</option>
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215 <option value="2">Trypsin (no P rule)</option>
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216 <option value="3">Arg-C</option>
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217 <option value="4">Arg-C (no P rule)</option>
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218 <option value="5">Arg-N</option>
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219 <option value="6">Glu-C</option>
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220 <option value="7">Lys-C</option>
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221 </param>
2
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222 <param name="max_missed_cleavages" argument="-c" type="integer" value="2" label="Max Missed Cleavages" help="The max missed cleavages" />
0
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223 </section>
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224 <section name="search" title="PSM" expanded="false">
2
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225 <param name="frag_method" argument="-fragmentMethod" type="select" label="Fragmentation Method">
0
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226 <option value="1" selected="true">CID/HCD</option>
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227 <option value="2">ETD</option>
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228 </param>
2
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229 <param name="scoring_method" argument="-m" type="select" label="Scoring Method">
0
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230 <option value="1" selected="true">HyperScore</option>
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231 <option value="2">MVH</option>
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232 </param>
2
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233 <param name="max_charge" argument="-maxCharge" type="integer" value="3" label="Max Charge" help="The maximum charge to consider if the charge state is not available" />
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234 <param name="min_charge" argument="-minCharge" type="integer" value="2" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available" />
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235 <param name="min_peaks" argument="-minPeaks" type="integer" value="10" label="Minimum Peaks" help="Min peaks in spectrum" />
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236 <param name="min_score" argument="-minScore" type="integer" value="12" label="Minimum Score" help="Minimum score to consider for peptide searching" />
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237 <param name="max_length" argument="-maxLength" type="integer" value="45" label="Maximum length of peptide" help="The maximum length of peptide to consider." />
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238 <param name="num_random_peptides" argument="-n" type="integer" value="1000" label="Number of Random Peptides" help="The number of random peptides" />
0
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239 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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240 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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241 <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"
galaxyp
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242 </inputs>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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243 <outputs>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
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244 <data name="query_tags" format="tabular" from_work_dir="qry.tags" label="${tool.name} on ${on_string}: tag file">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
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245 <filter>req_inputs['tags']['tagType'] in ['pFind']</filter>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
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246 </data>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
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247 <data name="psm_annotation" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: PSM Annotation">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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248 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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249 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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250 <action name="column_names" type="metadata" default="peptide,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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251 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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252 </data>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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parents: 1
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253 <data name="detail" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: Detail">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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254 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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255 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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256 <action name="column_names" type="metadata" default="${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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257 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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258 </data>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
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259 <data name="psm" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: PSM">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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260 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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261 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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262 <action name="column_names" type="metadata" default="peptide,modification,n,${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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263 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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264 </data>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
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265 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: PSM Rank (txt)">
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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266 <actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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267 <action name="comment_lines" type="metadata" default="1" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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268 <action name="column_names" type="metadata" default="peptide,modification,n,${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"
galaxyp
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269 </actions>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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270 </data>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
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271 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: PSM Rank (mgf)"/>
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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272 </outputs>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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273 <tests>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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274 <!-- Test-1 -->
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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275 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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276 <section name="req_inputs">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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277 <conditional name="input_type">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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278 <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
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279 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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280 <param name="peptide_input_selector" value="single" />
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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281 <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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282 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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283 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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284 <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
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diff changeset
285 <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
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286 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
287 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
288 <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
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diff changeset
289 <param name="var_mod" value="117"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
290 <param name="max_mods" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
291 <param name="unmodified" value="False"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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292 <param name="aa" value="True"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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293 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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294 <section name="ms_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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295 <section name="tolerance_params">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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296 <param name="precursor_tolerance" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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297 <param name="precursor_unit" value="ppm"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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298 <param name="tolerance" value="0.6"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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299 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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300 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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301 <param name="enzyme" value="0"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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302 <param name="max_missed_cleavages" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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303 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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304 <section name="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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305 <param name="frag_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
306 <param name="scoring_method" value="1"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
307 <param name="max_charge" value="3"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
308 <param name="min_charge" value="2"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
309 <param name="min_peaks" value="10"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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diff changeset
310 <param name="min_score" value="12"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
311 <param name="max_length" value="45"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
312 <param name="num_random_peptides" value="1000"/>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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313 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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314 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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diff changeset
315 <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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diff changeset
316 <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
317 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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318 <has_text text="ELGSSDLTAR" />
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
319 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\tiTRAQ_f4.mgf\t2\t2\t1191.6\d+\t2.0\d+\t1191.62\d+\t596.81\d+\t18.68\d+\t0\t20\t5\t995\t0.006\d+\t1"/>
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
320 </assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
321 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
322 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
323
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
324 <!-- Test-2 -->
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
325 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
326 <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
327 <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
328 <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
329 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
330 <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
331 <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
332 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
333 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
334 <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
335 <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
336 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
337 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
338 <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
339 <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
340 <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
341 <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
342 <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
343 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
344 <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
345 <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
346 <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
347 <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
348 <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
349 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
350 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
351 <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
352 <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
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="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
355 <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
356 <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
357 <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
358 <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
359 <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
360 <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
361 <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
362 <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
363 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
364 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
365 <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
366 <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
367 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
368 <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
369 <has_text text="SPYREFTDHLVK" />
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
370 <has_line_matching expression="SPYREFTDHLVK\tiTRAQ 4-plex of K@12\S+;iTRAQ 4-plex of peptide N-term@0\S+\t1\tiTRAQ_f4.mgf\t4\t3\t1778.\d+\t3.02\d+\t1778.95\d+\t593.99\d+\t12.17\d+\t2\t14\t-1\t-1\t100.0\t1"/>
0
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 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
373 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
374
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
375 <!-- Test-3 -->
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
376 <test>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
377 <section name="req_inputs">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
378 <conditional name="input_type">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
379 <param name="input_type_selector" value="peptide"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
380 <conditional name="multiple">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
381 <param name="peptide_input_selector" value="multiple" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
382 <param name="input" ftype="tabular" value="novel_peptides"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
383 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
384 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
385 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
386 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
387 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
388 <section name="modifications">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
389 <param name="fixed_mod" value="6,103,157"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
390 <param name="var_mod" value="117"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
391 <param name="max_mods" value="3"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
392 <param name="unmodified" value="True"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
393 <param name="aa" value="True"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
394 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
395 <section name="ms_params">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
396 <section name="tolerance_params">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
397 <param name="precursor_tolerance" value="10"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
398 <param name="precursor_unit" value="ppm"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
399 <param name="tolerance" value="0.6"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
400 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
401 <section name="digestion">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
402 <param name="enzyme" value="0"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
403 <param name="max_missed_cleavages" value="1"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
404 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
405 <section name="search">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
406 <param name="frag_method" value="1"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
407 <param name="scoring_method" value="1"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
408 <param name="max_charge" value="3"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
409 <param name="min_charge" value="2"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
410 <param name="min_peaks" value="7"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
411 <param name="min_score" value="10"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
412 <param name="max_length" value="45"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
413 <param name="num_random_peptides" value="1000"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
414 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
415 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
416 <param name="report_spectrum_file" value="false"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
417 <output name="psm_rank_txt">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
418 <assert_contents>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
419 <has_text text="ELGSSDLTAR" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
420 <has_text text="SPYREFTDHLVK" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
421 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\t3\t2\t1191.6\d+\t-3.04\d+\t1191.62\d+\t596.8\d+\t24.18\d+\t0\t22\t1\t995\t0.002\d+\t1\t0\tYes" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
422 </assert_contents>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
423 </output>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
424 </test>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
425
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
426 <!-- Test-4 -->
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
427 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
428 <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
429 <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
430 <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
431 <conditional name="multiple">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
432 <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
433 <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
434 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
435 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
436 <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
437 <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
438 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
439 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
440 <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
441 <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
442 <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
443 <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
444 <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
445 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
446 <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
447 <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
448 <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
449 <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
450 <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
451 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
452 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
453 <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
454 <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
455 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
456 <section name="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 <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
464 <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
465 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
466 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
467 <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
468 <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
469 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
470 <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
471 <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
472 </assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
473 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
474 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
475
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
476 <!-- Test-5 -->
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
477 <test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
478 <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
479 <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
480 <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
481 <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
482 </conditional>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
483 <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
484 <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
485 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
486 <section name="modifications">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
487 <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
488 <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
489 <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
490 <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
491 <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
492 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
493 <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
494 <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
495 <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
496 <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
497 <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
498 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
499 <section name="digestion">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
500 <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
501 <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
502 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
503 <section name="search">
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
504 <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
505 <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
506 <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
507 <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
508 <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
509 <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
510 <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
511 <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
512 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
513 </section>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
514 <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
515 <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
516 <assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
517 <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
518 </assert_contents>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
519 </output>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
520 </test>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
521
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
522 <!-- Test-6 -->
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
523 <test>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
524 <section name="req_inputs">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
525 <conditional name="input_type">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
526 <param name="input_type_selector" value="peptide"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
527 <conditional name="multiple">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
528 <param name="peptide_input_selector" value="multiple" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
529 <param name="input" ftype="tabular" value="novel_peptides"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
530 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
531 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
532 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
533 <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
534 <param name="indexType" value="2"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
535 <conditional name="tags">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
536 <param name="tagType" value="PepQuery"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
537 <param name="tag_file" ftype="tabular" value="test.tags"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
538 <param name="tagIndexType" value="2"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
539 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
540 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
541 <section name="modifications">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
542 <param name="fixed_mod" value=""/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
543 <param name="var_mod" value="117,114,118,128"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
544 <param name="max_mods" value="3"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
545 <param name="unmodified" value="True"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
546 <param name="aa" value="True"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
547 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
548 <section name="ms_params">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
549 <section name="tolerance_params">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
550 <param name="precursor_tolerance" value="20"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
551 <param name="precursor_unit" value="ppm"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
552 <param name="tolerance" value="0.02"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
553 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
554 <section name="digestion">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
555 <param name="enzyme" value="0"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
556 <param name="max_missed_cleavages" value="0"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
557 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
558 <section name="search">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
559 <param name="frag_method" value="1"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
560 <param name="scoring_method" value="1"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
561 <param name="max_charge" value="3"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
562 <param name="min_charge" value="2"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
563 <param name="min_peaks" value="10"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
564 <param name="min_score" value="12"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
565 <param name="max_length" value="25"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
566 <param name="num_random_peptides" value="1000"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
567 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
568 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
569 <param name="report_spectrum_file" value="true"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
570 <output name="psm_rank_txt">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
571 <assert_contents>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
572 <has_text text="MTDRHAGTY" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
573 <has_text text="controllerType=0 controllerNumber=1 scan=19905" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
574 </assert_contents>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
575 </output>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
576 </test>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
577
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
578 <!-- Test-7 -->
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
579 <test>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
580 <section name="req_inputs">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
581 <conditional name="input_type">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
582 <param name="input_type_selector" value="peptide"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
583 <conditional name="multiple">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
584 <param name="peptide_input_selector" value="multiple" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
585 <param name="input" ftype="tabular" value="novel_peptides"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
586 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
587 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
588 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
589 <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
590 <param name="indexType" value="2"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
591 <conditional name="tags">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
592 <param name="tagType" value="pFind"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
593 <param name="qry_res" ftype="txt" value="pFind.qry.res"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
594 </conditional>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
595 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
596 <section name="modifications">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
597 <param name="fixed_mod" value=""/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
598 <param name="var_mod" value="117,114,118,128"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
599 <param name="max_mods" value="3"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
600 <param name="unmodified" value="True"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
601 <param name="aa" value="True"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
602 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
603 <section name="ms_params">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
604 <section name="tolerance_params">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
605 <param name="precursor_tolerance" value="20"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
606 <param name="precursor_unit" value="ppm"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
607 <param name="tolerance" value="0.02"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
608 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
609 <section name="digestion">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
610 <param name="enzyme" value="0"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
611 <param name="max_missed_cleavages" value="0"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
612 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
613 <section name="search">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
614 <param name="frag_method" value="1"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
615 <param name="scoring_method" value="1"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
616 <param name="max_charge" value="3"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
617 <param name="min_charge" value="2"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
618 <param name="min_peaks" value="10"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
619 <param name="min_score" value="12"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
620 <param name="max_length" value="25"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
621 <param name="num_random_peptides" value="1000"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
622 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
623 </section>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
624 <param name="report_spectrum_file" value="true"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
625 <output name="psm_rank_txt">
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
626 <assert_contents>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
627 <has_text text="MTDRHAGTY" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
628 <has_text text="controllerType=0 controllerNumber=1 scan=19905" />
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
629 </assert_contents>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
630 </output>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
631 <output name="query_tags" file="test.tags"/>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
632 <!--
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
633 -->
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
634 </test>
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
635
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
636 </tests>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
637 <help><![CDATA[
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
638 **PepQuery**
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
639
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
640 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.
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
641
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
642 **Inputs**
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
643 - 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
parents:
diff changeset
644
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
645 - 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
parents:
diff changeset
646 - 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
parents:
diff changeset
647 - 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
parents:
diff changeset
648
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
649 - A mass spectrometry MGF file
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
650 - A reference protein fasta database, peptides matching a reference sequence will be excluded.
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
651 - An optional tags file for no-enzyme immunopeptidomics search
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
652
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
653 - See: http://pepquery.org/data/PepQuery_for_immunopeptidomics_data.pdf
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
654
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
655 **Outputs**
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
656 - PSM annotation - tabular with columns:
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
657
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
658 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
659
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
660 - Detail - tabular with columns:
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
661
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
662 - *report_spectrum_file* spectrum_title peptide modification pep_mass score
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
663
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
664 - PSM - tabular with columns:
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
665
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
666 - 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
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
667
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
668 - PSM Rank - tabular with columns:
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
669
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
670 - 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*
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
671
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
672 - 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
parents:
diff changeset
673
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
674 The *report_spectrum_file* is an optional field that can be added.
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
675
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
676 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
parents:
diff changeset
677
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
678 .. _PepQuery: http://pepquery.org/document.html
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
679
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
680 ]]></help>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
681 <citations>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
682 <citation type="doi">10.1101/gr.235028.118</citation>
2
5b5a9f59e2c7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents: 1
diff changeset
683 <citation type="doi">10.1038/s41467-020-15456-w</citation>
0
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
684 </citations>
32d3818fc635 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
685 </tool>