Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 13:4b85ea34afae draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:44:31 -0500
parents 8bf84c4cb1cb
children 231687cac31b
comparison
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12:8bf84c4cb1cb 13:4b85ea34afae
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 hicBuildMatrix 14 @BINARY@
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 $restrictionCutFileBinSize_conditional.binSize 28 --binSize
29 #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
30 '${repeat.binSize}'
31 #end for
29 #end if 32 #end if
30 33
31 34
32 #if $restrictionSequence: 35 #if $restrictionSequence:
33 --restrictionSequence '$restrictionSequence' 36 --restrictionSequence '$restrictionSequence'
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 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
92 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate 95 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
93 is too far away from the nearest restriction site." /> 96 is too far away from the nearest restriction site." />
94 </when> 97 </when>
95 <when value="optionBinSize"> 98 <when value="optionBinSize">
96 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp" 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.
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. 100 Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
98 Otherwise all reads in the interval are considered. "/> 101 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"/>
102 </repeat>
99 </when> 103 </when>
100 </conditional> 104 </conditional>
101 105
102 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" 106 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
103 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or 107 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
156 <repeat name="samFiles"> 160 <repeat name="samFiles">
157 <param name="samFile" value="small_test_R2_unsorted.sam"/> 161 <param name="samFile" value="small_test_R2_unsorted.sam"/>
158 </repeat> 162 </repeat>
159 <conditional name="restrictionCutFileBinSize_conditional"> 163 <conditional name="restrictionCutFileBinSize_conditional">
160 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/> 164 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
161 <param name="binSize" value="5000"/> 165 <repeat name='binSizes'>
166 <param name="binSize" value="5000"/>
167 </repeat>
162 </conditional> 168 </conditional>
163 <param name='outputFormat' value='h5'/> 169 <param name='outputFormat' value='h5'/>
164 <param name='outBam_Boolean' value="True" /> 170 <param name='outBam_Boolean' value="True" />
165 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> 171 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
166 <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size" delta="50000"/> 172 <output name="outFileName" ftype="h5">
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>
167 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/> 200 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
168 </test> 201 </test>
169 </tests> 202 </tests>
170 <help><![CDATA[ 203 <help><![CDATA[
171 204