Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 7:be42758f532e draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
author iuc
date Wed, 03 Jan 2018 13:28:16 -0500
parents 30d427846764
children 707f691c974c
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6:30d427846764 7:be42758f532e
1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1"> 1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.2">
2 <description>creates a contact matrix</description> 2 <description>creates a contact matrix</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicBuildMatrix</token> 4 <token name="@BINARY@">hicBuildMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
35 35
36 #if $region: 36 #if $region:
37 --region '$region' 37 --region '$region'
38 #end if 38 #end if
39 39
40 #if $outputFormat == 'h5' 40 --outFileName matrix.$outputFormat
41 --outFileName matrix.h5 41
42 #elif $outputFormat == 'cool'
43 --outFileName matrix.cool
44 #end if
45 --outBam ./unsorted.bam 42 --outBam ./unsorted.bam
46 43
47 $keepSelfCircles 44 $keepSelfCircles
48 45
49 #if $minMappingQuality and $minMappingQuality is not None: 46 #if $minMappingQuality and $minMappingQuality is not None:
60 && 57 &&
61 mv ./QCfolder/* $qc.files_path/ 58 mv ./QCfolder/* $qc.files_path/
62 && 59 &&
63 mv $qc.files_path/hicQC.html $qc 60 mv $qc.files_path/hicQC.html $qc
64 && mv $qc.files_path/*.log raw_qc 61 && mv $qc.files_path/*.log raw_qc
62 && mv matrix.$outputFormat matrix
65 && samtools sort ./unsorted.bam -o sorted.bam 63 && samtools sort ./unsorted.bam -o sorted.bam
66 64
67 ]]> 65 ]]>
68 </command> 66 </command>
69 <inputs> 67 <inputs>
120 <option value="cool">cool</option> 118 <option value="cool">cool</option>
121 </param> 119 </param>
122 </inputs> 120 </inputs>
123 <outputs> 121 <outputs>
124 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/> 122 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
125 <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"> 123 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
126 <filter>outputFormat == 'h5'</filter> 124 <change_format>
127 </data> 125 <when input="outputFormat" value="cool" format="cool" />
128 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}"> 126 </change_format>
129 <filter>outputFormat == 'cool'</filter>
130 </data> 127 </data>
131 <data name="qc" format="html" label="${tool.name} QC"/> 128 <data name="qc" format="html" label="${tool.name} QC"/>
132 <data name="raw_qc" from_work_dir='raw_qc' label="${tool.name} raw QC" /> 129
130 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC" />
133 </outputs> 131 </outputs>
134 <tests> 132 <tests>
135 <test> 133 <test>
136 <repeat name="samFiles"> 134 <repeat name="samFiles">
137 <param name="samFile" value="small_test_R1_unsorted.sam"/> 135 <param name="samFile" value="small_test_R1_unsorted.sam"/>
144 <param name="binSize" value="5000"/> 142 <param name="binSize" value="5000"/>
145 </conditional> 143 </conditional>
146 <param name='outputFormat' value='h5'/> 144 <param name='outputFormat' value='h5'/>
147 145
148 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> 146 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
149 <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/> 147 <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
150 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/> 148 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
151 </test> 149 </test>
152 </tests> 150 </tests>
153 <help><![CDATA[ 151 <help><![CDATA[
154 152
210 - long range 208 - long range
211 209
212 Read orientation: 210 Read orientation:
213 _________________ 211 _________________
214 - inward pairs 212 - inward pairs
215 - outward pairs 213 - outward pairs
216 - left pairs 214 - left pairs
217 - right pairs 215 - right pairs
218 216
219 .. image:: $PATH_TO_IMAGES/hicQC.png 217 .. image:: $PATH_TO_IMAGES/hicQC.png
220 :width: 70 % 218 :width: 70 %