Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix
comparison hicBuildMatrix.xml @ 21:ed2cca6b5de4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author | iuc |
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date | Wed, 18 Oct 2023 10:48:01 +0000 |
parents | 9edf8894a22d |
children | a4c13ddcc8ee |
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20:29f66c353bcb | 21:ed2cca6b5de4 |
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50 #if $outBam: | 50 #if $outBam: |
51 $outBam ./unsorted.bam | 51 $outBam ./unsorted.bam |
52 #end if | 52 #end if |
53 | 53 |
54 $keepSelfCircles | 54 $keepSelfCircles |
55 $removeSelfLigation | 55 $keepSelfLigation |
56 $skipDuplicationCheck | 56 $skipDuplicationCheck |
57 | 57 |
58 #if $minMappingQuality and $minMappingQuality is not None: | 58 #if $minMappingQuality and $minMappingQuality is not None: |
59 --minMappingQuality $minMappingQuality | 59 --minMappingQuality $minMappingQuality |
60 #end if | 60 #end if |
94 <param argument="--maxLibraryInsertSize" type="integer" optional="true" value="" label="Maximum library insert size defines different cut offs based on the maximum expected library size" help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer) | 94 <param argument="--maxLibraryInsertSize" type="integer" optional="true" value="" label="Maximum library insert size defines different cut offs based on the maximum expected library size" help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer) |
95 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 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 |
96 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate | 96 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate |
97 is too far away from the nearest restriction site." /> | 97 is too far away from the nearest restriction site." /> |
98 | 98 |
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. | 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. |
100 Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file."> | 100 Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file."> |
101 <param argument="--binSize" type="integer" optional="true" value="" label="Bin size in bp" /> | 101 <param argument="--binSize" type="integer" optional="true" value="" label="Bin size in bp" /> |
102 </repeat> | 102 </repeat> |
103 | 103 |
104 <expand macro="region" /> | 104 <expand macro="region" /> |
105 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." /> | 105 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." /> |
106 <param argument="--removeSelfLigation" type="boolean" truevalue="--removeSelfLigation" falsevalue="" label="remove self ligation" help="If set, inward facing reads less than 1000 bp apart and having a restriction site in between are removed. Although this reads do not contribute to any distant contact, they are useful to account for bias in the data" /> | 106 <param argument="--keepSelfLigation" type="boolean" truevalue="--keepSelfLigation" falsevalue="" label="Keep self ligation" help="If set, inward facing reads less than 1000 bp apart and having a restriction site in between are kept. Although this reads do not contribute to any distant contact, they are useful to account for bias in the data." /> |
107 <expand macro="minMappingQuality" /> | 107 <expand macro="minMappingQuality" /> |
108 <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." /> | 108 <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." /> |
109 <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected | 109 <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected |
110 Usually the sizes can be determined from the SAM/BAM input files, however, | 110 Usually the sizes can be determined from the SAM/BAM input files, however, |
111 for cHi-C or scHi-C it can be that at the start or end no data is present. | 111 for cHi-C or scHi-C it can be that at the start or end no data is present. |
112 Please consider that this option causes that only reads are considered which are on the listed chromosomes. | 112 Please consider that this option causes that only reads are considered which are on the listed chromosomes. |
113 Use this option to guarantee fixed sizes. An example file is available via UCSC: | 113 Use this option to guarantee fixed sizes. An example file is available via UCSC: |
114 http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" /> | 114 http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" /> |
115 | 115 |
116 <param argument='--outBam' type='boolean' truevalue='--outBam' falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam | 116 <param argument="--outBam" type="boolean" truevalue="--outBam" falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam |
117 file containing all valid Hi-C reads can be created | 117 file containing all valid Hi-C reads can be created |
118 using this option. This bam file could be useful to | 118 using this option. This bam file could be useful to |
119 inspect the distribution of valid Hi-C reads pairs or | 119 inspect the distribution of valid Hi-C reads pairs or |
120 for other downstream analyses, but is not used by any | 120 for other downstream analyses, but is not used by any |
121 HiCExplorer tool. Computation will be significantly | 121 HiCExplorer tool. Computation will be significantly |
122 longer if this option is set." /> | 122 longer if this option is set." /> |
123 | 123 |
124 <param name='outputFormat' type='select' label="Output file format"> | 124 <param name="outputFormat" type="select" label="Output file format"> |
125 <option value='h5'>HiCExplorer format</option> | 125 <option value="h5">HiCExplorer format</option> |
126 <option value="cool">cool</option> | 126 <option value="cool">cool</option> |
127 </param> | 127 </param> |
128 </inputs> | 128 </inputs> |
129 <outputs> | 129 <outputs> |
130 <data name="outfileBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"> | 130 <data name="outfileBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"> |
134 <change_format> | 134 <change_format> |
135 <when input="outputFormat" value="cool" format="cool" /> | 135 <when input="outputFormat" value="cool" format="cool" /> |
136 </change_format> | 136 </change_format> |
137 </data> | 137 </data> |
138 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" /> | 138 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" /> |
139 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" /> | 139 <data name="raw_qc" from_work_dir="raw_qc" format="txt" label="${tool.name} raw QC on ${on_string}" /> |
140 </outputs> | 140 </outputs> |
141 <tests> | 141 <tests> |
142 <test expect_num_outputs="4"> | 142 <test expect_num_outputs="4"> |
143 <repeat name="samFiles"> | 143 <repeat name="samFiles"> |
144 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> | 144 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> |
145 </repeat> | 145 </repeat> |
146 <repeat name="samFiles"> | 146 <repeat name="samFiles"> |
147 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> | 147 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> |
148 </repeat> | 148 </repeat> |
149 <param name='outputFormat' value='h5' /> | 149 <param name="outputFormat" value="h5" /> |
150 <repeat name='binSizes'> | 150 <repeat name="binSizes"> |
151 <param name="binSize" value="5000" /> | 151 <param name="binSize" value="5000" /> |
152 </repeat> | 152 </repeat> |
153 <param name='restrictionCutFile' value='DpnII_10k.bed' /> | 153 <param name="restrictionCutFile" value="DpnII_10k.bed" /> |
154 <param name='restrictionSequence' value='GATC' /> | 154 <param name="restrictionSequence" value="GATC" /> |
155 <param name='danglingSequence' value='GATC' /> | 155 <param name="danglingSequence" value="GATC" /> |
156 <param name='outBam' value="True" /> | 156 <param name="outBam" value="True" /> |
157 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" /> | 157 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" /> |
158 <output name="outFileName" ftype="h5"> | 158 <output name="outFileName" ftype="h5"> |
159 <assert_contents> | 159 <assert_contents> |
160 <has_h5_keys keys='intervals,matrix' /> | 160 <has_h5_keys keys="intervals,matrix" /> |
161 </assert_contents> | 161 </assert_contents> |
162 </output> | 162 </output> |
163 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2' /> | 163 <output name="raw_qc" file="raw_qc_report" compare="diff" lines_diff="2" /> |
164 </test> | 164 </test> |
165 <test expect_num_outputs="4"> | 165 <test expect_num_outputs="4"> |
166 <repeat name="samFiles"> | 166 <repeat name="samFiles"> |
167 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> | 167 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> |
168 </repeat> | 168 </repeat> |
169 <repeat name="samFiles"> | 169 <repeat name="samFiles"> |
170 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> | 170 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> |
171 </repeat> | 171 </repeat> |
172 <repeat name='binSizes'> | 172 <repeat name="binSizes"> |
173 <param name="binSize" value="5000" /> | 173 <param name="binSize" value="5000" /> |
174 </repeat> | 174 </repeat> |
175 <param name='restrictionCutFile' value='DpnII_10k.bed' /> | 175 <param name="restrictionCutFile" value="DpnII_10k.bed" /> |
176 <param name='restrictionSequence' value='GATC' /> | 176 <param name="restrictionSequence" value="GATC" /> |
177 <param name='danglingSequence' value='GATC' /> | 177 <param name="danglingSequence" value="GATC" /> |
178 <param name='outputFormat' value='cool' /> | 178 <param name="outputFormat" value="cool" /> |
179 <param name='outBam' value="True" /> | 179 <param name="outBam" value="True" /> |
180 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" /> | 180 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" /> |
181 <output name="outFileName" ftype="cool"> | 181 <output name="outFileName" ftype="cool"> |
182 <assert_contents> | 182 <assert_contents> |
183 <has_h5_keys keys='bins,chroms,indexes,pixels' /> | 183 <has_h5_keys keys="bins,chroms,indexes,pixels" /> |
184 </assert_contents> | 184 </assert_contents> |
185 </output> | 185 </output> |
186 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2' /> | 186 <output name="raw_qc" file="raw_qc_report" compare="diff" lines_diff="2" /> |
187 </test> | 187 </test> |
188 </tests> | 188 </tests> |
189 <help><![CDATA[ | 189 <help><![CDATA[ |
190 | 190 |
191 Creation of the contact matrix | 191 Creation of the contact matrix |