Mercurial > repos > iuc > merquryfk_hapmaker
changeset 0:87a0eb97d160 draft
planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
| author | iuc |
|---|---|
| date | Wed, 19 Feb 2025 11:21:46 +0000 |
| parents | |
| children | 67d3299eaee4 |
| files | hapmaker.xml macros.xml test-data/child.tar test-data/maternal.hap.ktab test-data/maternal.tar test-data/paternal.hap.ktab test-data/paternal.tar |
| diffstat | 5 files changed, 146 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hapmaker.xml Wed Feb 19 11:21:46 2025 +0000 @@ -0,0 +1,64 @@ +<tool id="merquryfk_hapmaker" name="MerquryFK HAPmaker" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> + <description>Generates hap-mer tables from FastK k-mer data of maternal, paternal, and child sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p input_files + && mkdir -p hapmaker_ktabs + && ln -s '$maternal_ktab_tar' maternal.tar + && tar -xf maternal.tar + && mv ktabfiles ktabfiles_maternal + && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab + && mv "\$(find ktabfiles_maternal -type f -name '*.ktab.1')" "input_files/.maternal.ktab.1" + && ln -s '$paternal_ktab_tar' paternal.tar + && tar -xf paternal.tar + && mv ktabfiles ktabfiles_paternal + && mv ktabfiles_paternal/output.ktab input_files/paternal.ktab + && mv "\$(find ktabfiles_paternal -type f -name '*.ktab.1')" "input_files/.paternal.ktab.1" + && ln -s '$child_ktab_tar' child.tar + && tar -xf child.tar + && mv ktabfiles ktabfiles_child + && mv ktabfiles_child/output.ktab input_files/child.ktab + && mv "\$(find ktabfiles_child -type f -name '*.ktab.1')" "input_files/.child.ktab.1" + && HAPmaker -v + -T\${GALAXY_SLOTS:-4} + input_files/maternal.ktab + input_files/paternal.ktab + input_files/child.ktab + && mv input_files/.*.hap* hapmaker_ktabs + && tar -czvf HapK_ktab_files.tar.gz hapmaker_ktabs + ]]></command> + <inputs> + <param name="maternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of maternal ktab file from FastK"/> + <param name="paternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of paternal ktab file from FastK"/> + <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/> + </inputs> + <outputs> + <data name="paternal_out" format="fastk_ktab" from_work_dir="paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/> + <data name="maternal_out" format="fastk_ktab" from_work_dir="maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/> + <data name="intermediate_ktab" format="fastk_ktab_tar" from_work_dir="HapK_ktab_files.tar.gz" label="${tool.name} on ${on_string}: HapMaker Intermediate Ktab files"/> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" value="maternal.tar"/> + <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" value="paternal.tar"/> + <param name="child_ktab_tar" ftype="fastk_ktab_tar" value="child.tar"/> + <output name="paternal_out" value="paternal.hap.ktab"/> + <output name="maternal_out" value="maternal.hap.ktab"/> + <output name="intermediate_ktab" ftype="fastk_ktab_tar"> + <assert_contents> + <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/> + <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + HAPmaker generates hap-mer tables for parental datasets for merquryfk pipeline. Before running HAPplot or MerquryFK in trio mode, it is necessary to generate a table of hap-mers + for both the mother and father, using FastK k-mer tables from the maternal, paternal, and child sequence data sets. + The output of this process produces two k-mer tables: <mat>.hap.ktab for the maternal hap-mers and <pat>.hap.ktab for the paternal hap-mers. + ]]></help> + <expand macro="citation"/> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Feb 19 11:21:46 2025 +0000 @@ -0,0 +1,82 @@ +<macros> + <token name="@VERSION@">1.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PLOTS@"> + -w${width} + -h${height} + </token> + <token name="@MEASURE@"> + #if $measure.measurement == "relative": + -x${max_x} + -y${max_y} + #else: + -X${max_x} + -Y${max_y} + #end if + </token> + <token name="@GRAPHS@"> + #for $graph in $graphs: + $graph + #end for + </token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">merquryfk</requirement> + </requirements> + </xml> + <xml name="sizes"> + <conditional name="measure"> + <param name="measurement" type="select" label="How would you like to set max value?"> + <option value="absolute">Absolute terms</option> + <option value="relative">Relative to peak</option> + </param> + <when value="absolute"> + <param name="max_x" type="integer" min="0" label="Max X value" optional="true" value="2"/> + <param name="max_y" type="integer" min="0" label="Max Y value" optional="true" value="1"/> + </when> + <when value="relative"> + <param name="max_x" type="float" min="0" label="Max X multiplier" optional="true" value="2.1" help="Sets max value as assigned multiple of count 'peak' away from origin"/> + <param name="max_y" type="float" min="0" label="Max Y multiplier" optional="true" value="1.1" help="Sets max value as assigned multiple of count 'peak' away from origin"/> + </when> + </conditional> + </xml> + <xml name="plots"> + <param name="width" label="Width of plots" type="float" optional="true" value="6.0" min="0"/> + <param name="height" label="Height of plots" type="float" optional="true" value="4.5" min="0"/> + </xml> + <xml name="graphs"> + <param name="graphs" label="What graphs would you like to generate?" type="select" multiple="true" help="If none are selected, all will be generated"> + <option value="-l">Line plot</option> + <option value="-f">Fill plot</option> + <option value="-s">Stack plot</option> + <option value="-z">K-mer counts unique to assembly</option> + </param> + </xml> + <xml name="graphs2"> + <param name="graphs" label="What graphs would you like to generate?" type="select" multiple="true" help="If none are selected, all will be generated"> + <option value="-l">Line plot</option> + <option value="-f">Fill plot</option> + <option value="-s">Stack plot</option> + </param> + </xml> + <xml name="pdf"> + <param argument="-pdf" type="boolean" label="PDF Output" truevalue="-pdf" falsevalue="" help="Output in pdf format if true, png if false"/> + </xml> + <xml name="description"> + <description>part of MERQURY.FK</description> + </xml> + <xml name="citation"> + <citations> + <citation type="bibtex"> + @misc{githubMERQURY.FK. + author = {Eugene Myers}, + year = {2023}, + title = {MERQURY.FK}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/thegenemyers/MERQURY.FK}, + } + </citation> + </citations> + </xml> +</macros> \ No newline at end of file