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comparison idpassemble.xml @ 5:39eaac8f3f42 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
author galaxyp
date Tue, 21 Nov 2017 13:19:10 -0500
parents 123813b3eed3
children 4b418a632bb0
comparison
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4:123813b3eed3 5:39eaac8f3f42
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="idpassemble" name="idpAssemble" version="@VERSION@.1"> 2 <tool id="idpassemble" name="idpAssemble" version="@VERSION@.0">
3 <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description> 3 <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
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 30
31 #if $AssignSourceHierarchy 31 #if $AssignSourceHierarchyCondition.HasAssignSourceHierarchy
32 -AssignSourceHierarchy '$AssignSourceHierarchy' 32 -AssignSourceHierarchy '$AssignSourceHierarchyCondition.AssignSourceHierarchy'
33 #end if 33 #end if
34 34
35 #if $IsobaricSampleMapping 35 #if $IsobaricSampleMappingCondition.HasIsobaricSampleMapping
36 -IsobaricSampleMapping '$IsobaricSampleMapping' 36 -IsobaricSampleMapping '$IsobaricSampleMappingCondition.IsobaricSampleMapping'
37 #end if 37 #end if
38 38
39 #if len($input) > 1 39 #if len($input) > 1
40 -MergedOutputFilepath output 40 -MergedOutputFilepath output
41 #for $i in $input 41 #for $i in $input
63 </when> 63 </when>
64 </conditional> 64 </conditional>
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." /> 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." />
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." /> 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." />
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." /> 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." /> 68
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." /> 69 <conditional name="AssignSourceHierarchyCondition">
70 <param name="HasAssignSourceHierarchy" type="boolean" truevalue="1" falsevalue="0" label="Assign sources to a hierarchy?"/>
71 <when value="1">
72 <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." />
73 </when>
74 <when value="0">
75 </when>
76 </conditional>
77 <conditional name="IsobaricSampleMappingCondition">
78 <param name="HasIsobaricSampleMapping" type="boolean" truevalue="1" falsevalue="0" label="Assign sample names to reporter ions?"/>
79 <when value="1">
80 <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." />
81 </when>
82 <when value="0">
83 </when>
84 </conditional>
70 </inputs> 85 </inputs>
71 <outputs> 86 <outputs>
72 <data format="idpdb" name="output" from_work_dir="output" /> 87 <data format="idpdb" name="output" from_work_dir="output" />
73 </outputs> 88 </outputs>
74 <tests> 89 <tests>
101 <param name="filter_at_gene_level_condition.MinSpectra" value="2" /> 116 <param name="filter_at_gene_level_condition.MinSpectra" value="2" />
102 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" /> 117 <param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
103 <param name="MinSpectraPerDistinctMatch" value="1" /> 118 <param name="MinSpectraPerDistinctMatch" value="1" />
104 <param name="MinSpectraPerDistinctPeptide" value="1" /> 119 <param name="MinSpectraPerDistinctPeptide" value="1" />
105 <param name="MaxProteinGroupsPerPeptide" value="10" /> 120 <param name="MaxProteinGroupsPerPeptide" value="10" />
121 <param name="HasAssignSourceHierarchy" value="1" />
106 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" /> 122 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
107 <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" /> 123 <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" />
108 </test> 124 </test>
109 <test> 125 <test>
110 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" /> 126 <param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
117 <param name="MaxProteinGroupsPerPeptide" value="10" /> 133 <param name="MaxProteinGroupsPerPeptide" value="10" />
118 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" /> 134 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
119 </test> 135 </test>
120 <test> 136 <test>
121 <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" /> 137 <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" />
138 <param name="HasAssignSourceHierarchy" value="1" />
139 <param name="HasIsobaricSampleMapping" value="1" />
122 <param name="IsobaricSampleMapping" value="mapping.tsv" ftype="tabular" /> 140 <param name="IsobaricSampleMapping" value="mapping.tsv" ftype="tabular" />
123 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" /> 141 <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
124 <output name="output" file="201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB" compare="sim_size" delta="500000" /> 142 <output name="output" file="201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB" compare="sim_size" delta="500000" />
125 </test> 143 </test>
126 </tests> 144 </tests>
128 <![CDATA[ 146 <![CDATA[
129 **What it does** 147 **What it does**
130 148
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. 149 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.
132 150
151 ====
133 152
134 **AssignSourceHierarchy** 153 **AssignSourceHierarchy**
154
135 The assembly file is a tab-delimited file with two columns that organizes the sources (individual runs) into a hierarchy. 155 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. 156 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). 157 A forward slash in the group name adds another level to the hierarchy (just like a directory path).
138 158
139 *A simple example:* 159 *A simple example:*
140 ====== =========== 160
141 /repA repA1.idpDB 161 ::
142 /repA repA2.idpDB 162
143 /repB repB1.idpDB 163 /repA repA1.idpDB
144 /repB repB2.idpDB 164 /repA repA2.idpDB
145 ====== =========== 165 /repB repB1.idpDB
166 /repB repB2.idpDB
167
146 168
147 *A multi-level example:* 169 *A multi-level example:*
148 ===== =========== 170
149 /A/1 A1_f1 171 ::
150 /A/1 A1_f2 172
151 /A/2 A2_f1 173 /A/1 A1_f1
152 /A/2 A2_f2 174 /A/1 A1_f2
153 /B/1 B1_f1 175 /A/2 A2_f1
154 /B/1 B1_f2 176 /A/2 A2_f2
155 /B/2 B2_f1 177 /B/1 B1_f1
156 /B/2 B2_f2 178 /B/1 B1_f2
157 ===== =========== 179 /B/2 B2_f1
158 180 /B/2 B2_f2
181
182 ====
159 183
160 **IsobaricSampleMapping** 184 **IsobaricSampleMapping**
185
161 The mapping file is a tab-delimited file with two columns. The first column is the full path to a source group, 186 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 187 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 188 sample name *Reference*, if present, will be used to normalize the other channels. Samples named *Empty* will be
164 ignored. 189 ignored.
165 190
191
166 *iTRAQ-4plex example:* 192 *iTRAQ-4plex example:*
167 =============================== ========================== 193
168 /Case/Group1_A123_B456_C789 A123,B456,C789,Reference 194 ::
169 /Case/Group2_D123_E456_F789 D123,E456,F789,Reference 195
170 /Control/Group3_X123_Y456_Z789 Reference,X123,Y456,Z789 196 /Case/Group1_A123_B456_C789 A123,B456,C789,Reference
171 /Control/Group4_U123_V456 U123,Reference,V456,Empty 197 /Case/Group2_D123_E456_F789 D123,E456,F789,Reference
172 =============================== ========================== 198 /Ctrl/Group3_X123_Y456_Z789 Reference,X123,Y456,Z789
199 /Ctrl/Group4_U123_V456_None U123,Reference,V456,Empty
200
173 201
174 *TMT-10plex example:* 202 *TMT-10plex example:*
175 ============================= ================================================================================ 203
176 /Group1_Cases1-4_Controls1-4 Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference 204 ::
177 /Group2_Cases5-8_Controls5-8 Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference 205
178 ============================= ================================================================================ 206 /Group1_Cases1-4_Controls1-4 Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference
207 /Group2_Cases5-8_Controls5-8 Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference
179 208
180 ]]> 209 ]]>
181 </help> 210 </help>
182 <citations> 211 <citations>
183 <citation type="doi">10.1021/pr900360j</citation> 212 <citation type="doi">10.1021/pr900360j</citation>