| Previous changeset 2:4a841ab67e3b (2023-04-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b |
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modified:
macros.xml scHicQualityControl.xml |
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| diff -r 4a841ab67e3b -r e426ba8aeb93 macros.xml --- a/macros.xml Fri Apr 14 14:22:47 2023 +0000 +++ b/macros.xml Thu Jul 31 16:49:35 2025 +0000 |
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| @@ -3,6 +3,12 @@ <token name="@TOOL_VERSION@">4</token> <token name="@PROFILE@">22.05</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">hicexplorer</xref> + </xrefs> + </xml> + <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">schicexplorer</requirement> @@ -173,4 +179,4 @@ <option value="plasma_r">plasma reversed</option> </param> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r 4a841ab67e3b -r e426ba8aeb93 scHicQualityControl.xml --- a/scHicQualityControl.xml Fri Apr 14 14:22:47 2023 +0000 +++ b/scHicQualityControl.xml Thu Jul 31 16:49:35 2025 +0000 |
| [ |
| b'@@ -4,6 +4,7 @@\n <token name="@BINARY@">scHicQualityControl</token>\n <import>macros.xml</import>\n </macros>\n+ <expand macro="xrefs"/>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n ## https://github.com/open2c/cooler/issues/299\n@@ -21,7 +22,7 @@\n --maximumRegionToConsider $maximumRegionToConsider\n #if $dpi:\n --dpi $dpi\n- #end if \n+ #end if\n --outFileNameDensity plot_density.$image_file_format\n --outFileNameReadCoverage plot_read_coverage.$image_file_format\n --outFileNameQCReport report.txt\n@@ -36,9 +37,9 @@\n ]]></command>\n <inputs>\n <expand macro="matrix_scooler_macro"/>\n- <param name="minimumReadCoverage" type="integer" value="1000000" label="Minimum read coverage" help=\'Remove all samples with a lower read coverage as this value.\' /> \n- <param name="minimumDensity" type="float" value="0.001" label="Minimum density" help=\'Remove all samples with a lower density as this value.\' /> \n- <param name="maximumRegionToConsider" type="integer" value="30000000" label="Maximum region to consider" help=\'To compute the density, consider only this genomic distance around the diagonal.\' /> \n+ <param name="minimumReadCoverage" type="integer" value="1000000" label="Minimum read coverage" help=\'Remove all samples with a lower read coverage as this value.\' />\n+ <param name="minimumDensity" type="float" value="0.001" label="Minimum density" help=\'Remove all samples with a lower density as this value.\' />\n+ <param name="maximumRegionToConsider" type="integer" value="30000000" label="Maximum region to consider" help=\'To compute the density, consider only this genomic distance around the diagonal.\' />\n <param name=\'chromosomes\' type=\'text\' label=\'List of chromosomes to consider\' help=\'Please separate the chromosomes by space\'/>\n <param name=\'dpi\' type=\'integer\' label=\'DPI for image\' help=\'Change the default resolution of the plot.\' optional=\'true\'/>\n <param name="image_file_format" type="select" label="Image output format">\n@@ -62,7 +63,7 @@\n </data>\n <data name="report" from_work_dir="report.txt" format="txt" label="${tool.name} on ${on_string}: QC report"/>\n <data name="outFileName" from_work_dir="filtered_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Filtered matrices"/>\n- \n+\n </outputs>\n <tests>\n <test>\n@@ -72,83 +73,83 @@\n <param name=\'maximumRegionToConsider\' value=\'30000000\' />\n <param name="image_file_format" value="png" />\n <param name="dpi" value="300" />\n- <output name="output_plot_density" file="scHicQualityControl/density.png" ftype="png" compare="sim_size" delta="35000"/> \n- <output name="output_plot_read_coverage" file="scHicQualityControl/coverage.png" ftype="png" compare="sim_size" delta="35000"/> \n- <output name="report" file="scHicQualityControl/qc_report.txt" ftype="txt" compare="sim_size" delta="35000"/> \n+ <output name="output_plot_density" file="scHicQualityControl/density.png" ftype="png" compare="sim_size" delta="35000"/>\n+ <output name="output_plot_read_coverage" file="scHicQualityControl/coverage.png" ftype="png" compare="sim_size" delta="35000"/>\n+ <output name="report" file="scHicQualityControl/qc_report.txt" ftype="txt" compare="sim_size" delta="35000"/>\n <output name="outFileName" ftype="scool">\n <assert_contents>\n <has_h5_keys keys=\'Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins,\n- Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, \n- Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_A'..b"loid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/chrom_offset, \n- Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin1_id, \n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/length,\n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/name, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes,\n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/chrom_offset,\n+ Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin1_id,\n Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/count,\n- Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins, \n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins,\n Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/end,\n Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms,\n Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/name,\n- Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/bin1_offset, \n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/bin1_offset,\n Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels,\n- Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin2_id, \n+ Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin2_id,\n Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz,\n- Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/chrom, \n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/chrom,\n Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/start,\n- Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/length, \n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/length,\n Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes,\n- Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/chrom_offset, \n- Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin1_id, \n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/chrom_offset,\n+ Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin1_id,\n Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/count'/></assert_contents>\n </output>\n </test>\n" |