| Previous changeset 4:09c589057ee8 (2023-08-10) Next changeset 6:eb7b00ec347d (2024-04-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7 |
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added:
merqury_plot_CN.xml test-data/output_merqury.assembly_01.only.tabular test-data/output_merqury.assembly_01.spectra-cn.tabular |
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| diff -r 09c589057ee8 -r d7edbc9c3a07 merqury_plot_CN.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merqury_plot_CN.xml Fri Feb 16 22:00:00 2024 +0000 |
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| @@ -0,0 +1,105 @@ +<tool id="merquryplot" name="Merqury histogram plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>evaluate the assembly quality</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <version_command>merqury --version</version_command> + + <command detect_errors="exit_code"><![CDATA[ + mkdir -p output_files/ && + \$MERQURY/plot/plot_spectra_cn.R + -f '$input1' + -o output_files/merqury_plot + #if $z + --zero-hist '$z' + #end if + #if $cutoff + --cutoff '$cutoff' + #end if + --xdim $xdim + --ydim $ydim + #if $xmax>0 + --xmax $xmax + #end if + #if $ymax>0 + --ymax $ymax + #end if + --type $type + #if $output_selector=='pdf' + -p + #end if + + ]]> </command> + <inputs> + <param argument="-f" type="data" name="input1" format="tabular" /> + <param argument="--xdim" type="integer" label="Width of plot" value="6" min="0" /> + <param argument="--ydim" type="integer" label="Height of plot" value="5" min="0" /> + <param argument="--xmax" type="float" label="Maximum limit for k-mer multiplicity (leave 0 for default)" value="0" min="0" help="default: (x where y=peak) * 2.1" /> + <param argument="--ymax" type="float" label="Maximum limit for k-mer count (leave 0 for default)" value="0" min="0" help="default: (y where y=peak) * 1.1" /> + <param argument="-z" type="data" label="Assembly only counts" format="tabular" help=".only.hist file " optional="true" /> + <param argument="--cutoff" type="data" label="Solid k-mer cutoffs" format="txt" help="cutoff.txt file" optional="true" /> + <param name="output_selector" type="select" label="Output format" argument="-p"> + <option value="png" selected="true">PNG</option> + <option value="pdf">PDF</option> + </param> + <param argument="--type" type="select" label="Type of plot (default all)"> + <option value="all" selected="true">All</option> + <option value="line">Line</option> + <option value="fill">Fill</option> + <option value="stack">Stack</option> + </param> + </inputs> + <outputs> + <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png plots"> + <discover_datasets pattern="(?P<name>.+)\.png" format="png" directory="output_files"/> + <filter>"png" in output_selector</filter> + </collection> + <collection name="pdf_files" type="list" label="${tool.name} on ${on_string}: pdf plots"> + <discover_datasets pattern="(?P<name>.+)\.pdf" format="pdf" directory="output_files"/> + <filter>"pdf" in output_selector</filter> + </collection> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input1" value="output_merqury.assembly_01.spectra-cn.tabular"/> + <param name="xdim" value="6" /> + <param name="ydim" value="5" /> + <param name="xmax" value="0" /> + <param name="ymax" value="0" /> + <param name="z" value="output_merqury.assembly_01.only.tabular"/> + <param name="type" value="all" /> + <param name="output_selector" value="png" /> + <output_collection name="png_files" type="list" count="3"> + <element name="merqury_plot.fl"> + <assert_contents> + <has_size value="99000" delta="5000"/> + </assert_contents> + </element> + <element name="merqury_plot.ln"> + <assert_contents> + <has_size value="99000" delta="5000"/> + </assert_contents> + </element> + <element name="merqury_plot.st"> + <assert_contents> + <has_size value="124000" delta="20000"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**Purpose** +Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be +generated. Inputs : Histogram files generated by merqury. + + ]]> </help> + <expand macro="citations"/> +</tool> + |
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| diff -r 09c589057ee8 -r d7edbc9c3a07 test-data/output_merqury.assembly_01.only.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_merqury.assembly_01.only.tabular Fri Feb 16 22:00:00 2024 +0000 |
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| diff -r 09c589057ee8 -r d7edbc9c3a07 test-data/output_merqury.assembly_01.spectra-cn.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_merqury.assembly_01.spectra-cn.tabular Fri Feb 16 22:00:00 2024 +0000 |
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