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comparison computeMatrixOperations.xml @ 10:848ce8f81e6e draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb
author bgruening
date Mon, 09 Jul 2018 18:55:26 -0400
parents 1638c02b28b5
children be95d48dd27f
comparison
equal deleted inserted replaced
9:d8c2a68643ce 10:848ce8f81e6e
10 @BINARY@ 10 @BINARY@
11 #if $submodule.command == "info": 11 #if $submodule.command == "info":
12 info 12 info
13 -m $submodule.matrixFile 13 -m $submodule.matrixFile
14 > $outFileTxt 14 > $outFileTxt
15 #else if $submodule.command == "relabel":
16 relabel
17 -m $submodule.matrixFile
18 #if $submodule.groupLabels is not None and str($submodule.groupLabels) != '':
19 --groupLabels $submodule.groupLabels
20 #end if
21 #if $submodule.sampleLabels is not None and str($submodule.sampleLabels) != '':
22 --sampleLabels $submodule.sampleLabels
23 #end if
15 #else if $submodule.command == "subset": 24 #else if $submodule.command == "subset":
16 subset 25 subset
17 -m $submodule.matrixFile 26 -m $submodule.matrixFile
18 #if $submodule.groups is not None and str($submodule.groups) != '': 27 #if $submodule.groups is not None and str($submodule.groups) != '':
19 --groups $submodule.groups 28 --groups $submodule.groups
24 -o $outFileName 33 -o $outFileName
25 #else if $submodule.command == "filterStrand": 34 #else if $submodule.command == "filterStrand":
26 filterStrand 35 filterStrand
27 -m $submodule.matrixFile 36 -m $submodule.matrixFile
28 --strand $submodule.strand 37 --strand $submodule.strand
38 -o $outFileName
39 #else if $submodule.command == "filterValues":
40 filterValues
41 -m $submodule.matrixFile
42 #if $submodule.minValue is not None and str($submodule.minValue) != '':
43 --min $submodule.minValue
44 #end if
45 #if $submodule.maxValue is not None and str($submodule.maxValue) != '':
46 --max $submodule.maxValue
47 #end if
29 -o $outFileName 48 -o $outFileName
30 #else if $submodule.command == "rbind": 49 #else if $submodule.command == "rbind":
31 #set $files=[] 50 #set $files=[]
32 #for $f in $submodule.matrixFiles: 51 #for $f in $submodule.matrixFiles:
33 #silent $files.append(str($f.matrixFile)) 52 #silent $files.append(str($f.matrixFile))
57 </command> 76 </command>
58 <inputs> 77 <inputs>
59 <conditional name="submodule"> 78 <conditional name="submodule">
60 <param name="command" type="select" label="Operation type"> 79 <param name="command" type="select" label="Operation type">
61 <option value="info" selected="true">Print information (info)</option> 80 <option value="info" selected="true">Print information (info)</option>
81 <option value="relabel">Relabel the samples and/or groups (relabel)</option>
62 <option value="subset">Subset by samples and/or groups of regions (subset)</option> 82 <option value="subset">Subset by samples and/or groups of regions (subset)</option>
63 <option value="filterStrand">Filter by strand (filterStrand)</option> 83 <option value="filterStrand">Filter by strand (filterStrand)</option>
84 <option value="filterValues">Filter by min/max value (filterValues)</option>
64 <option value="rbind">Bind matrices, top to bottom (rbind)</option> 85 <option value="rbind">Bind matrices, top to bottom (rbind)</option>
65 <option value="cbind">Bind matrices, left to right (cbind)</option> 86 <option value="cbind">Bind matrices, left to right (cbind)</option>
66 <option value="sort">Sort by region order in specified files (sort)</option> 87 <option value="sort">Sort by region order in specified files (sort)</option>
67 </param> 88 </param>
68 <when value="info"> 89 <when value="info">
69 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" 90 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
70 label="Matrix file from the computeMatrix tool" help=""/> 91 label="Matrix file from the computeMatrix tool" help=""/>
71 </when> 92 </when>
72 93
94 <when value="relabel">
95 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
96 label="Matrix file from the computeMatrix tool" help=""/>
97 <param argument="groupLabels" type="text" optional="true" label="New Region/Group Labels."
98 help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each group of regions."/>
99 <param argument="sampleLabels" type="text" optional="true" label="New Sample Labels."
100 help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each sample."/>
101 </when>
102
73 <when value="subset"> 103 <when value="subset">
74 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" 104 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
75 label="Matrix file from the computeMatrix tool" help=""/> 105 label="Matrix file from the computeMatrix tool" help=""/>
76 <param argument="groups" type="text" optional="true" label="Region groups to include." 106 <param argument="groups" type="text" optional="true" label="Region groups to include."
77 help="If blank, all region groups are output. Alternatively, one or more groups listed in the output of the 'info' command can be used (separate groups by a space and enclose in quotes if needed)" /> 107 help="If blank, all region groups are output. Alternatively, one or more groups listed in the output of the 'info' command can be used (separate groups by a space and enclose in quotes if needed)" />
80 </when> 110 </when>
81 111
82 <when value="filterStrand"> 112 <when value="filterStrand">
83 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" 113 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
84 label="Matrix file from the computeMatrix tool" help=""/> 114 label="Matrix file from the computeMatrix tool" help=""/>
85 <param argument="strand" type="select" label="Only include regions on this strand." 115 <param argument="--strand" type="select" label="Only include regions on this strand."
86 help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation."> 116 help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation.">
87 <option value="+">+</option> 117 <option value="+">+</option>
88 <option value="-">-</option> 118 <option value="-">-</option>
89 <option value=".">. (no annotated strand)</option> 119 <option value=".">. (no annotated strand)</option>
90 </param> 120 </param>
121 </when>
122
123 <when value="filterValues">
124 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
125 label="Matrix file from the computeMatrix tool" help=""/>
126 <param argument="--min" type="float" optional="true" label="Minimum value"
127 help="Exclude any row in the matrix with a value below this. By default there is no minimum value." />
128 <param argument="--max" type="float" optional="true" label="Maximum value"
129 help="Exclude any row in the matrix with a value above this. By default there is no maximum value." />
91 </when> 130 </when>
92 131
93 <when value="rbind"> 132 <when value="rbind">
94 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2"> 133 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
95 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" 134 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"