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comparison computeMatrixOperations.xml @ 0:db94d629b9eb draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 07:50:45 -0500
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-1:000000000000 0:db94d629b9eb
1 <tool id="deeptools_compute_matrix_operations" name="computeMatrixOperations" version="@WRAPPER_VERSION@.0">
2 <description>Modify or combine the output of computeMatrix in a variety of ways.</description>
3 <macros>
4 <token name="@BINARY@">computeMatrixOperations</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command>
9 <![CDATA[
10 @BINARY@
11 #if $submodule.command == "info":
12 info
13 -m $submodule.matrixFile
14 > $outFileTxt
15 #else if $submodule.command == "subset":
16 subset
17 -m $submodule.matrixFile
18 #if $submodule.groups is not None and str($submodule.groups) != '':
19 --groups $submodule.groups
20 #end if
21 #if $submodule.samples is not None and str($submodule.samples) != '':
22 --samples $submodule.samples
23 #end if
24 -o $outFileName
25 #else if $submodule.command == "filterStrand":
26 filterStrand
27 -m $submodule.matrixFile
28 --strand $submodule.strand
29 -o $outFileName
30 #else if $submodule.command == "rbind":
31 #set $files=[]
32 #for $f in $submodule.matrixFiles:
33 #silent $files.append(str($f.matrixFile))
34 #end for
35 rbind
36 -m '#echo "' '".join($files)#'
37 -o $outFileName
38 #else if $submodule.command == "cbind":
39 cbind
40 #set $files=[]
41 #for $f in $submodule.matrixFiles:
42 #silent $files.append(str($f.matrixFile))
43 #end for
44 -m '#echo "' '".join($files)#'
45 -o $outFileName
46 #else if $submodule.command == "sort":
47 sort
48 #set $files=[]
49 #for $f in $submodule.regionsFiles:
50 #silent $files.append(str($f.regionsFile))
51 #end for
52 -m $submodule.matrixFile
53 -R '#echo "' '".join($files)#'
54 -o $outFileName
55 #end if
56 ]]>
57 </command>
58 <inputs>
59 <conditional name="submodule">
60 <param name="command" type="select" label="Operation type">
61 <option value="info" selected="true">Print information (info)</option>
62 <option value="subset">Subset by samples and/or groups of regions (subset)</option>
63 <option value="filterStrand">Filter by strand (filterStrand)</option>
64 <option value="rbind">Bind matrices, top to bottom (rbind)</option>
65 <option value="cbind">Bind matrices, left to right (cbind)</option>
66 <option value="sort">Sort by region order in specified files (sort)</option>
67 </param>
68 <when value="info">
69 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
70 label="Matrix file from the computeMatrix tool" help=""/>
71 </when>
72
73 <when value="subset">
74 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
75 label="Matrix file from the computeMatrix tool" help=""/>
76 <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)" />
78 <param argument="samples" type="text" optional="true" label="Samples to include."
79 help="If blank, all samples are output. Alternatively, one or more samples listed in the output of the 'info' command can be used (separate sample names by a space and enclose in quotes if needed)" />
80 </when>
81
82 <when value="filterStrand">
83 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
84 label="Matrix file from the computeMatrix tool" help=""/>
85 <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.">
87 <option value="+">+</option>
88 <option value="-">-</option>
89 <option value=".">. (no annotated strand)</option>
90 </param>
91 </when>
92
93 <when value="rbind">
94 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
95 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
96 label="Matrix file from the computeMatrix tool" help=""/>
97 </repeat>
98 </when>
99
100 <when value="cbind">
101 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
102 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
103 label="Matrix file from the computeMatrix tool" help=""/>
104 </repeat>
105 </when>
106
107 <when value="sort">
108 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
109 label="Matrix file from the computeMatrix tool" help=""/>
110 <repeat name="regionsFiles" title="BED or GTF files of regions" min="1">
111 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
112 help="File, in BED format, containing the regions to plot."/>
113 </repeat>
114 </when>
115 </conditional>
116 </inputs>
117 <outputs>
118 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}">
119 <filter>
120 ((
121 submodule['command'] != "info"
122 ))
123 </filter>
124 </data>
125 <data format="txt" name="outFileTxt" label="${tool.name} info on ${on_string}">
126 <filter>
127 ((
128 submodule['command'] == "info"
129 ))
130 </filter>
131 </data>
132 </outputs>
133 <tests>
134 <test>
135 <param name="command" value="info" />
136 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
137 <output name="outFileTxt" file="computeMatrixOperations.txt" ftype="txt" />
138 </test>
139 <test>
140 <param name="command" value="rbind" />
141 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
142 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
143 <output name="outFileName" file="computeMatrixOperations_result2.mat.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" delta="100"/>
144 </test>
145 </tests>
146 <help>
147 <![CDATA[
148
149 What it does
150 ------------
151
152 ``computeMatrixOperations`` can perform a variety of operations on one or more files produced by ``computeMatrix`` (N.B., the output is always written to a new file):
153
154 +----------------+--------------------------------------------------------------------------------------------------------------------------+
155 + **Subcommand** | **What it does** |
156 +----------------+--------------------------------------------------------------------------------------------------------------------------+
157 + info | Prints out the sample and region group names in the order in which they appear. |
158 +----------------+--------------------------------------------------------------------------------------------------------------------------+
159 + subset | Subsets a file by the desired samples/region group names. This can also change the order of these samples/region groups. |
160 +----------------+--------------------------------------------------------------------------------------------------------------------------+
161 + filterStrand | Filters the file to only include regions annotated as being on a particular strand. |
162 +----------------+--------------------------------------------------------------------------------------------------------------------------+
163 + rbind | Concatenates multiple matrices together, top to bottom. |
164 +----------------+--------------------------------------------------------------------------------------------------------------------------+
165 + cbind | Merges multiple matrices, left to right. |
166 +----------------+--------------------------------------------------------------------------------------------------------------------------+
167 + sort | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s). |
168 +----------------+--------------------------------------------------------------------------------------------------------------------------+
169
170
171 These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file.
172
173 -----
174
175 @REFERENCES@
176 ]]>
177 </help>
178 <expand macro="citations" />
179 </tool>