Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 26:3ef5a7dd1a36 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
author galaxyp
date Tue, 10 May 2016 06:33:08 -0400
parents 0986f68fb410
children 432140bcc7fe
comparison
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25:0986f68fb410 26:3ef5a7dd1a36
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.10.0">
2 <description> 2 <description>
3 Perform protein identification using various search engines based on results from SearchGUI 3 Perform protein identification using various search engines based on results from SearchGUI
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="1.1">peptide_shaker</requirement> 9 <requirement type="package" version="1.10">peptide_shaker</requirement>
10 </requirements> 10 </requirements>
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <command> 12 <command>
13 <![CDATA[ 13 <![CDATA[
14 #from datetime import datetime 14 #from datetime import datetime
45 -species_update 1 45 -species_update 1
46 #end if 46 #end if
47 47
48 ##Optional processing parameters: 48 ##Optional processing parameters:
49 #if $processing_options.processing_options_selector == "yes" 49 #if $processing_options.processing_options_selector == "yes"
50 -protein_FDR "${processing_options.protein_fdr}" 50 -protein_fdr "${processing_options.protein_fdr}"
51 -peptide_FDR "${processing_options.peptide_fdr}" 51 -peptide_fdr "${processing_options.peptide_fdr}"
52 -psm_FDR "${processing_options.psm_fdr}" 52 -psm_fdr "${processing_options.psm_fdr}"
53 -ptm_score "${processing_options.ptm_score.ptm_score_selector}" 53 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
54 #if $processing_options.ptm_score.ptm_score_selector == 1 54 #if $processing_options.ptm_score.ptm_score_selector == 1
55 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" 55 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
56 #if str($processing_options.ptm_score.ptm_threshold) != '' 56 #if str($processing_options.ptm_score.ptm_threshold) != ''
57 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" 57 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
60 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" 60 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
61 #end if 61 #end if
62 62
63 ##Optional filtering parameters: 63 ##Optional filtering parameters:
64 #if $filtering_options.filtering_options_selector == "yes": 64 #if $filtering_options.filtering_options_selector == "yes":
65 -min_peptide_length "${filtering_options.min_peptide_length}" 65 -import_peptide_length_min "${filtering_options.min_peptide_length}"
66 -max_peptide_length "${filtering_options.max_peptide_length}" 66 -import_peptide_length_max "${filtering_options.max_peptide_length}"
67 -max_precursor_error "${filtering_options.max_precursor_error}" 67 -import_precurosor_mz "${filtering_options.max_precursor_error}"
68 -max_precursor_error_type "${filtering_options.max_precursor_error_type}" 68 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
69 ##-max_xtandem_e "${filtering_options.max_xtandem_e}" 69 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
70 ##-max_omssa_e "${filtering_options.max_omssa_e}" 70 ##-max_omssa_e "${filtering_options.max_omssa_e}"
71 ##-max_mascot_e "${filtering_options.max_mascot_e}" 71 ##-max_mascot_e "${filtering_options.max_mascot_e}"
72 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" 72 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
73 #end if 73 #end if
491 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" /> 491 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
492 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> 492 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
493 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" 493 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
494 help="Next option specifies units (Da or ppm)" /> 494 help="Next option specifies units (Da or ppm)" />
495 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> 495 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
496 <option value="0">ppm</option> 496 <option value="1">ppm</option>
497 <option value="1">Daltons</option> 497 <option value="0">Daltons</option>
498 </param> 498 </param>
499 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /--> 499 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
500 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /--> 500 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
501 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /--> 501 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
502 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 502 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />