Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 15:f90c9c383fb2 draft

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"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
author bgruening
date Mon, 16 Dec 2019 13:19:21 +0000
parents d5c7bf85dd93
children 1a38e937b5ce
comparison
equal deleted inserted replaced
14:d5c7bf85dd93 15:f90c9c383fb2
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 11
12 mkdir ./QCfolder && 12 mkdir ./QCfolder &&
13 mkdir $qc.files_path && 13 mkdir $qc.files_path &&
14 @BINARY@ 14 hicBuildMatrix
15 15
16 --samFiles 16 --samFiles
17 #for $repeat in $samFiles: 17 #for $repeat in $samFiles:
18 '${repeat.samFile}' 18 '${repeat.samFile}'
19 #end for 19 #end for
23 --minDistance $restrictionCutFileBinSize_conditional.minDistance 23 --minDistance $restrictionCutFileBinSize_conditional.minDistance
24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize 24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
25 #end if 25 #end if
26 26
27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize": 27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
28 --binSize 28 --binSize $restrictionCutFileBinSize_conditional.binSize
29 #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
30 '${repeat.binSize}'
31 #end for
32 #end if 29 #end if
33 30
34 31
35 #if $restrictionSequence: 32 #if $restrictionSequence:
36 --restrictionSequence '$restrictionSequence' 33 --restrictionSequence '$restrictionSequence'
94 which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates 91 which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
95 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate 92 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
96 is too far away from the nearest restriction site." /> 93 is too far away from the nearest restriction site." />
97 </when> 94 </when>
98 <when value="optionBinSize"> 95 <when value="optionBinSize">
99 <repeat name='binSizes' title='Bin size in bp' min="1" help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites. 96 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"
100 Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file."> 97 help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
101 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"/> 98 Otherwise all reads in the interval are considered. "/>
102 </repeat>
103 </when> 99 </when>
104 </conditional> 100 </conditional>
105 101
106 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" 102 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
107 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or 103 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
160 <repeat name="samFiles"> 156 <repeat name="samFiles">
161 <param name="samFile" value="small_test_R2_unsorted.sam"/> 157 <param name="samFile" value="small_test_R2_unsorted.sam"/>
162 </repeat> 158 </repeat>
163 <conditional name="restrictionCutFileBinSize_conditional"> 159 <conditional name="restrictionCutFileBinSize_conditional">
164 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/> 160 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
165 <repeat name='binSizes'> 161 <param name="binSize" value="5000"/>
166 <param name="binSize" value="5000"/>
167 </repeat>
168 </conditional> 162 </conditional>
169 <param name='outputFormat' value='h5'/> 163 <param name='outputFormat' value='h5'/>
170 <param name='outBam_Boolean' value="True" /> 164 <param name='outBam_Boolean' value="True" />
171 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> 165 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
172 <output name="outFileName" ftype="h5"> 166 <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size" delta="50000"/>
173 <assert_contents>
174 <has_h5_keys keys='intervals,matrix'/>
175 </assert_contents>
176 </output>
177 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
178 </test>
179 <test>
180 <repeat name="samFiles">
181 <param name="samFile" value="small_test_R1_unsorted.sam"/>
182 </repeat>
183 <repeat name="samFiles">
184 <param name="samFile" value="small_test_R2_unsorted.sam"/>
185 </repeat>
186 <conditional name="restrictionCutFileBinSize_conditional">
187 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
188 <repeat name='binSizes'>
189 <param name="binSize" value="5000"/>
190 </repeat>
191 </conditional>
192 <param name='outputFormat' value='cool'/>
193 <param name='outBam_Boolean' value="True" />
194 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
195 <output name="outFileName" ftype="cool">
196 <assert_contents>
197 <has_h5_keys keys='bins,chroms,indexes,pixels'/>
198 </assert_contents>
199 </output>
200 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/> 167 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
201 </test> 168 </test>
202 </tests> 169 </tests>
203 <help><![CDATA[ 170 <help><![CDATA[
204 171