Mercurial > repos > iuc > schicexplorer_schicqualitycontrol

comparison scHicQualityControl.xml @ 3:e426ba8aeb93 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
author iuc
date Thu, 31 Jul 2025 16:49:35 +0000
parents 4a841ab67e3b
children
comparison
equal deleted inserted replaced
2:4a841ab67e3b 3:e426ba8aeb93
2 <description>quality control for single-cell Hi-C interaction matrices</description> 2 <description>quality control for single-cell Hi-C interaction matrices</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">scHicQualityControl</token> 4 <token name="@BINARY@">scHicQualityControl</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="xrefs"/>
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 ## https://github.com/open2c/cooler/issues/299 10 ## https://github.com/open2c/cooler/issues/299
10 cp '$matrix_scooler' matrix.scooler && 11 cp '$matrix_scooler' matrix.scooler &&
11 12
19 --minimumReadCoverage $minimumReadCoverage 20 --minimumReadCoverage $minimumReadCoverage
20 --minimumDensity $minimumDensity 21 --minimumDensity $minimumDensity
21 --maximumRegionToConsider $maximumRegionToConsider 22 --maximumRegionToConsider $maximumRegionToConsider
22 #if $dpi: 23 #if $dpi:
23 --dpi $dpi 24 --dpi $dpi
24 #end if 25 #end if
25 --outFileNameDensity plot_density.$image_file_format 26 --outFileNameDensity plot_density.$image_file_format
26 --outFileNameReadCoverage plot_read_coverage.$image_file_format 27 --outFileNameReadCoverage plot_read_coverage.$image_file_format
27 --outFileNameQCReport report.txt 28 --outFileNameQCReport report.txt
28 --outputScool filtered_matrices.scool 29 --outputScool filtered_matrices.scool
29 30
34 35
35 36
36 ]]></command> 37 ]]></command>
37 <inputs> 38 <inputs>
38 <expand macro="matrix_scooler_macro"/> 39 <expand macro="matrix_scooler_macro"/>
39 <param name="minimumReadCoverage" type="integer" value="1000000" label="Minimum read coverage" help='Remove all samples with a lower read coverage as this value.' /> 40 <param name="minimumReadCoverage" type="integer" value="1000000" label="Minimum read coverage" help='Remove all samples with a lower read coverage as this value.' />
40 <param name="minimumDensity" type="float" value="0.001" label="Minimum density" help='Remove all samples with a lower density as this value.' /> 41 <param name="minimumDensity" type="float" value="0.001" label="Minimum density" help='Remove all samples with a lower density as this value.' />
41 <param name="maximumRegionToConsider" type="integer" value="30000000" label="Maximum region to consider" help='To compute the density, consider only this genomic distance around the diagonal.' /> 42 <param name="maximumRegionToConsider" type="integer" value="30000000" label="Maximum region to consider" help='To compute the density, consider only this genomic distance around the diagonal.' />
42 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> 43 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
43 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 44 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
44 <param name="image_file_format" type="select" label="Image output format"> 45 <param name="image_file_format" type="select" label="Image output format">
45 <option value="png" selected="True">png</option> 46 <option value="png" selected="True">png</option>
46 <option value="svg">svg</option> 47 <option value="svg">svg</option>
60 <when input="image_file_format" value="pdf" format="pdf" /> 61 <when input="image_file_format" value="pdf" format="pdf" />
61 </change_format> 62 </change_format>
62 </data> 63 </data>
63 <data name="report" from_work_dir="report.txt" format="txt" label="${tool.name} on ${on_string}: QC report"/> 64 <data name="report" from_work_dir="report.txt" format="txt" label="${tool.name} on ${on_string}: QC report"/>
64 <data name="outFileName" from_work_dir="filtered_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Filtered matrices"/> 65 <data name="outFileName" from_work_dir="filtered_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Filtered matrices"/>
65 66
66 </outputs> 67 </outputs>
67 <tests> 68 <tests>
68 <test> 69 <test>
69 <param name='matrix_scooler' value='test_matrix.scool' /> 70 <param name='matrix_scooler' value='test_matrix.scool' />
70 <param name='minimumReadCoverage' value='100000' /> 71 <param name='minimumReadCoverage' value='100000' />
71 <param name='minimumDensity' value='0.001' /> 72 <param name='minimumDensity' value='0.001' />
72 <param name='maximumRegionToConsider' value='30000000' /> 73 <param name='maximumRegionToConsider' value='30000000' />
73 <param name="image_file_format" value="png" /> 74 <param name="image_file_format" value="png" />
74 <param name="dpi" value="300" /> 75 <param name="dpi" value="300" />
75 <output name="output_plot_density" file="scHicQualityControl/density.png" ftype="png" compare="sim_size" delta="35000"/> 76 <output name="output_plot_density" file="scHicQualityControl/density.png" ftype="png" compare="sim_size" delta="35000"/>
76 <output name="output_plot_read_coverage" file="scHicQualityControl/coverage.png" ftype="png" compare="sim_size" delta="35000"/> 77 <output name="output_plot_read_coverage" file="scHicQualityControl/coverage.png" ftype="png" compare="sim_size" delta="35000"/>
77 <output name="report" file="scHicQualityControl/qc_report.txt" ftype="txt" compare="sim_size" delta="35000"/> 78 <output name="report" file="scHicQualityControl/qc_report.txt" ftype="txt" compare="sim_size" delta="35000"/>
78 <output name="outFileName" ftype="scool"> 79 <output name="outFileName" ftype="scool">
79 <assert_contents> 80 <assert_contents>
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84 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/bin1_offset, 85 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
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131 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/chrom, 132 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/chrom,
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133 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/length, 134 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/length,
134 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/name, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes, 135 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/name, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes,
135 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/chrom_offset, 136 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/chrom_offset,
136 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin1_id, 137 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin1_id,
137 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/count, 138 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/count,
138 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins, 139 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins,
139 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/end, 140 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/end,
140 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms, 141 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms,
141 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/name, 142 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/name,
142 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/bin1_offset, 143 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/bin1_offset,
143 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels, 144 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels,
144 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin2_id, 145 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin2_id,
145 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz, 146 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz,
146 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/chrom, 147 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/chrom,
147 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/start, 148 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/start,
148 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/length, 149 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/length,
149 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes, 150 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes,
150 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/chrom_offset, 151 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/chrom_offset,
151 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin1_id, 152 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin1_id,
152 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/count'/></assert_contents> 153 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/count'/></assert_contents>
153 </output> 154 </output>
154 </test> 155 </test>
155 </tests> 156 </tests>
156 <help><![CDATA[ 157 <help><![CDATA[