Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 14:d5c7bf85dd93 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
author iuc
date Mon, 09 Dec 2019 10:27:01 +0000
parents ee5a82a286ed
children f90c9c383fb2
comparison
equal deleted inserted replaced
13:706936009fb7 14:d5c7bf85dd93
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>
7 <expand macro="requirements" > 7 <expand macro="requirements" >
8 <requirement type="package" version="1.6">samtools</requirement> 8 <requirement type="package" version="1.9">samtools</requirement>
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'
61 && 64 &&
62 mv $qc.files_path/hicQC.html $qc 65 mv $qc.files_path/hicQC.html $qc
63 && mv $qc.files_path/*.log raw_qc 66 && mv $qc.files_path/*.log raw_qc
64 && mv matrix.$outputFormat matrix 67 && mv matrix.$outputFormat matrix
65 #if $outBam_Boolean: 68 #if $outBam_Boolean:
66 && samtools sort ./unsorted.bam -o sorted.bam 69 && samtools sort -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
67 #end if 70 #end if
68 71
69 ]]> 72 ]]>
70 </command> 73 </command>
71 <inputs> 74 <inputs>
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"/> 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