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annotate idpassemble.xml @ 0:0d089906f752 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
author galaxyp
date Thu, 15 Dec 2016 17:12:33 -0500
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0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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1 <?xml version="1.0"?>
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2 <tool id="idpassemble" name="idpAssemble" version="@VERSION@.0">
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3 <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
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4 <macros>
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5 <import>macros.xml</import>
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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6 </macros>
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7 <expand macro="requirements" />
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Job Failed" />
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10 <regex match="^Error:.*$" source="both" level="fatal" />
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11 </stdio>
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12 <command>
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13 <![CDATA[
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14 #if len($input) < 2
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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15 cp '${input}' output &&
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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16 #end if
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17
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18 idpAssemble
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19 -MaxFDRScore $MaxFDRScore
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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20 -MinDistinctPeptides $filter_at_gene_level_condition.MinDistinctPeptides
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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21 -MinSpectra $filter_at_gene_level_condition.MinSpectra
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22 -MinAdditionalPeptides $filter_at_gene_level_condition.MinAdditionalPeptides
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23 -MinSpectraPerDistinctMatch $MinSpectraPerDistinctMatch
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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24 -MinSpectraPerDistinctPeptide $MinSpectraPerDistinctPeptide
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25 -MaxProteinGroupsPerPeptide $MaxProteinGroupsPerPeptide
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26 #if $filter_at_gene_level_condition.FilterAtGeneLevel
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27 -FilterAtGeneLevel 1
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28 #end if
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29 -SummarizeSources 1
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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30 #if len($input) > 1
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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31 -MergedOutputFilepath output
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32 #for $i in $input
0d089906f752 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpassemble commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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33 '${i.file_name}'
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34 #end for
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35 #else
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36 output
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37 #end if
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param name="input" type="data" format="idpdb" label="Input idpDB(s)" multiple="true"/>
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42 <param argument="-MaxFDRScore" type="float" label="Max FDR Score" min="0.00000001" value="0.05" help="Peptide-spectrum-matches (PSMs) with an FDR score (interpolated Q-value) higher than this will be excluded from the filtered data set." />
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43 <conditional name="filter_at_gene_level_condition">
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44 <param argument="-FilterAtGeneLevel" type="boolean" truevalue="1" falsevalue="0" label="Filter at Gene Level" help="Apply filters at the gene level (i.e. 'min distinct peptides per gene group' instead of 'min distinct peptides per protein group')"/>
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45 <when value="1">
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46 <param argument="-MinDistinctPeptides" type="integer" label="Min Distinct Peptides per Gene Group" min="1" value="2" help="Gene groups with fewer than this number of peptides will be excluded from the filtered data set." />
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47 <param argument="-MinSpectra" type="integer" label="Min Filtered Spectra per Gene Group" min="1" value="2" help="Gene groups with fewer than this number of spectra will be excluded from the filtered data set." />
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48 <param argument="-MinAdditionalPeptides" type="integer" label="Min Additional Peptides per Gene Group" min="0" value="1" help="Gene groups that are not necessary to explain the presence of at least this many extra peptides will be from the filtered data set. A value of 1 means that each gene group must explain at least 1 peptide that other gene groups do not explain." />
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49 </when>
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50 <when value="0">
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51 <param argument="-MinDistinctPeptides" type="integer" label="Min Distinct Peptides per Protein Group" min="1" value="2" help="Protein groups with fewer than this number of peptides will be excluded from the filtered data set." />
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52 <param argument="-MinSpectra" type="integer" label="Min Filtered Spectra per Protein Group" min="1" value="2" help="Protein groups with fewer than this number of spectra will be excluded from the filtered data set." />
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53 <param argument="-MinAdditionalPeptides" type="integer" label="Min Additional Peptides per Protein Group" min="0" value="1" help="Protein groups that are not necessary to explain the presence of at least this many extra peptides will be from the filtered data set. A value of 1 means that each protein group must explain at least 1 peptide that other protein groups do not explain." />
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54 </when>
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55 </conditional>
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56 <param argument="-MinSpectraPerDistinctMatch" type="integer" label="Min Filtered Spectra per Distinct Match" min="1" value="1" help="Distinct matches with fewer than this number of spectra will be excluded from the filtered data set." />
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57 <param argument="-MinSpectraPerDistinctPeptide" type="integer" label="Min Filtered Spectra per Distinct Peptide" min="1" value="1" help="Distinct peptides with fewer than this number of spectra will be excluded from the filtered data set." />
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58 <param argument="-MaxProteinGroupsPerPeptide" type="integer" label="Max Protein Groups per Distinct Peptide" min="0" value="10" help="Peptides that map to more than this number of protein groups will be excluded from the filtered data set. Highly ambiguous peptides are not very useful for quantitation." />
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59 </inputs>
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60 <outputs>
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61 <data format="idpdb" name="output" from_work_dir="output" />
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="input" value="201208-378803-mm.idpDB" />
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66 <param name="MaxFDRScore" value="0.05" />
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67 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
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68 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
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69 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
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70 <param name="MinSpectraPerDistinctMatch" value="1" />
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71 <param name="MinSpectraPerDistinctPeptide" value="1" />
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72 <param name="MaxProteinGroupsPerPeptide" value="10" />
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73 <output name="output" file="201208-378803-mm.idpDB" compare="sim_size" delta="500000" />
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74 </test>
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75 <test>
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76 <param name="input" value="201208-378803-msgf.idpDB" />
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77 <param name="MaxFDRScore" value="0.05" />
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78 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
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79 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
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80 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
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81 <param name="MinSpectraPerDistinctMatch" value="1" />
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82 <param name="MinSpectraPerDistinctPeptide" value="1" />
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83 <param name="MaxProteinGroupsPerPeptide" value="10" />
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84 <output name="output" file="201208-378803-msgf.idpDB" compare="sim_size" delta="500000" />
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85 </test>
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86 <test>
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87 <param name="input" value="201208-378803-cm.idpDB" />
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88 <param name="MaxFDRScore" value="0.05" />
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89 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
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90 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
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91 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
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92 <param name="MinSpectraPerDistinctMatch" value="1" />
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93 <param name="MinSpectraPerDistinctPeptide" value="1" />
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94 <param name="MaxProteinGroupsPerPeptide" value="10" />
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95 <output name="output" file="201208-378803-cm.idpDB" compare="sim_size" delta="500000" />
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96 </test>
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97 <test>
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98 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
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99 <param name="MaxFDRScore" value="0.05" />
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100 <param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
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101 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
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102 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
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103 <param name="MinSpectraPerDistinctMatch" value="1" />
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104 <param name="MinSpectraPerDistinctPeptide" value="1" />
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105 <param name="MaxProteinGroupsPerPeptide" value="10" />
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106 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
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107 </test>
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108 </tests>
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109 <help>
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110 <![CDATA[
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111 **What it does**
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112
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113 Merges and filters one or more IDPicker 3 idpDB files into a combined idpDB file. Protein assembly (e.g. parsimony) is conducted on the combined set of proteins.
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114 ]]>
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115 </help>
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116 <citations>
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117 <citation type="doi">10.1021/pr900360j</citation>
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118 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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119 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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120 </citations>
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121 </tool>