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comparison idpassemble.xml @ 3:d562ee284f8a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 82368da0ad9f7dcce4ce99a15c749eed915606ee
author galaxyp
date Thu, 02 Nov 2017 14:15:13 -0400
parents dd33125925d9
children 123813b3eed3
comparison
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2:dd33125925d9 3:d562ee284f8a
25 -MaxProteinGroupsPerPeptide $MaxProteinGroupsPerPeptide 25 -MaxProteinGroupsPerPeptide $MaxProteinGroupsPerPeptide
26 #if $filter_at_gene_level_condition.FilterAtGeneLevel 26 #if $filter_at_gene_level_condition.FilterAtGeneLevel
27 -FilterAtGeneLevel 1 27 -FilterAtGeneLevel 1
28 #end if 28 #end if
29 -SummarizeSources 1 29 -SummarizeSources 1
30
31 #if $AssignSourceHierarchy
32 -AssignSourceHierarchy '$AssignSourceHierarchy'
33 #end if
34
35 #if $IsobaricSampleMapping
36 -IsobaricSampleMapping '$IsobaricSampleMapping'
37 #end if
38
30 #if len($input) > 1 39 #if len($input) > 1
31 -MergedOutputFilepath output 40 -MergedOutputFilepath output
32 #for $i in $input 41 #for $i in $input
33 '${i.file_name}' 42 '${i.file_name}'
34 #end for 43 #end for
54 </when> 63 </when>
55 </conditional> 64 </conditional>
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." /> 65 <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." />
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." /> 66 <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." />
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." /> 67 <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." />
68 <param argument="-AssignSourceHierarchy" type="data" format="tabular" optional="true" label="Assign source files to groups" help="A tab-delimited file that organizes source files (e.g. individual runs in a fractionated experiment) into groups. See below for more details." />
69 <param argument="-IsobaricSampleMapping" type="data" format="tabular" optional="true" label="Assign sample names to reporter ions" help="A tab-delimited file that gives sample names to isobaric reporter ion channels (i.e. iTRAQ, TMT) across a given source group. See below for more details." />
59 </inputs> 70 </inputs>
60 <outputs> 71 <outputs>
61 <data format="idpdb" name="output" from_work_dir="output" /> 72 <data format="idpdb" name="output" from_work_dir="output" />
62 </outputs> 73 </outputs>
63 <tests> 74 <tests>
90 <param name="filter_at_gene_level_condition.MinSpectra" value="2" /> 101 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
91 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" /> 102 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
92 <param name="MinSpectraPerDistinctMatch" value="1" /> 103 <param name="MinSpectraPerDistinctMatch" value="1" />
93 <param name="MinSpectraPerDistinctPeptide" value="1" /> 104 <param name="MinSpectraPerDistinctPeptide" value="1" />
94 <param name="MaxProteinGroupsPerPeptide" value="10" /> 105 <param name="MaxProteinGroupsPerPeptide" value="10" />
106 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
95 <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" /> 107 <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" />
96 </test> 108 </test>
97 <test> 109 <test>
98 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" /> 110 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
99 <param name="MaxFDRScore" value="0.05" /> 111 <param name="MaxFDRScore" value="0.05" />
103 <param name="MinSpectraPerDistinctMatch" value="1" /> 115 <param name="MinSpectraPerDistinctMatch" value="1" />
104 <param name="MinSpectraPerDistinctPeptide" value="1" /> 116 <param name="MinSpectraPerDistinctPeptide" value="1" />
105 <param name="MaxProteinGroupsPerPeptide" value="10" /> 117 <param name="MaxProteinGroupsPerPeptide" value="10" />
106 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" /> 118 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
107 </test> 119 </test>
120 <test>
121 <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" />
122 <param name="IsobaricSampleMapping" value="mapping.tsv" ftype="tabular" />
123 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
124 <output name="output" file="201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB" compare="sim_size" delta="500000" />
125 </test>
108 </tests> 126 </tests>
109 <help> 127 <help>
110 <![CDATA[ 128 <![CDATA[
111 **What it does** 129 **What it does**
112 130
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. 131 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.
132
133
134 **AssignSourceHierarchy**
135 The assembly file is a tab-delimited file with two columns that organizes the sources (individual runs) into a hierarchy.
136 The first column is the name of a source group, the second column is the source path or name to assign to that group.
137 A forward slash in the group name adds another level to the hierarchy (just like a directory path).
138
139 *A simple example:*
140 ====== ===========
141 /repA repA1.idpDB
142 /repA repA2.idpDB
143 /repB repB1.idpDB
144 /repB repB2.idpDB
145 ====== ===========
146
147 *A multi-level example:*
148 ===== ===========
149 /A/1 A1_f1
150 /A/1 A1_f2
151 /A/2 A2_f1
152 /A/2 A2_f2
153 /B/1 B1_f1
154 /B/1 B1_f2
155 /B/2 B2_f1
156 /B/2 B2_f2
157 ===== ===========
158
159
160 **IsobaricSampleMapping**
161 The mapping file is a tab-delimited file with two columns. The first column is the full path to a source group,
162 the second column is a comma-delimited list of sample names, in ascending order of reporter ion mass. The special
163 sample name *Reference*, if present, will be used to normalize the other channels. Samples named *Empty* will be
164 ignored.
165
166 *iTRAQ-4plex example:*
167 =============================== ==========================
168 /Case/Group1_A123_B456_C789 A123,B456,C789,Reference
169 /Case/Group2_D123_E456_F789 D123,E456,F789,Reference
170 /Control/Group3_X123_Y456_Z789 Reference,X123,Y456,Z789
171 /Control/Group4_U123_V456 U123,Reference,V456,Empty
172 =============================== ==========================
173
174 *TMT-10plex example:*
175 ============================= ================================================================================
176 /Group1_Cases1-4_Controls1-4 Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference
177 /Group2_Cases5-8_Controls5-8 Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference
178 ============================= ================================================================================
179
114 ]]> 180 ]]>
115 </help> 181 </help>
116 <citations> 182 <citations>
117 <citation type="doi">10.1021/pr900360j</citation> 183 <citation type="doi">10.1021/pr900360j</citation>
118 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, 184 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},