Mercurial > repos > iuc > cactus_export
diff cactus_export.xml @ 0:a82a0acf4eb6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 827619d22d2931d8fb34ed6844cfa91433e1ac2c
| author | iuc |
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| date | Tue, 06 Feb 2024 00:30:57 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cactus_export.xml Tue Feb 06 00:30:57 2024 +0000 @@ -0,0 +1,156 @@ +<tool id="cactus_export" name="Cactus: export" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>whole-genome multiple sequence alignment to other formats</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + + ## check if the reference level was specified + #if $export_select.format in ['maf_selector', 'vg_selector']: + #if $export_select.ref_level == '': + echo "You must provide a reference level" && + exit 1 ; + #end if + #end if + + ln -s '$hal_file' alignment.hal + + ## make a MAF + #if $export_select.format == 'maf_selector': + && + hal2maf + --refGenome $export_select.ref_level + alignment.hal + alignment.maf + #end if + + ## make an assemblyHub + #if $export_select.format == 'ah_selector': + && + hal2assemblyHub.py + --maxCores \${GALAXY_SLOTS:-4} + --maxMemory \${GALAXY_MEMORY_MB:-8196}M + ./jobStore + alignment.hal + assemblyhub + && + tar -cv assemblyhub > assemblyhub.tar + #end if + + ## make a VG + #if $export_select.format == 'vg_selector': + && + hal2vg alignment.hal + --progress + > alignment.pg + #end if + + ]]></command> + <inputs> + <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus"/> + <conditional name="export_select"> + <param name="format" type="select" label="Output format" help="The type of output you want to export. Run this tool once for each output format."> + <option value="maf_selector" selected="true">MAF file</option> + <option value="ah_selector">Assembly Hub</option> + <option value="vg_selector">VG file</option> + </param> + <when value="maf_selector"> + <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/> + </when> + <when value="ah_selector"> + </when> + <when value="vg_selector"> + <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)"> + <filter>export_select['format'] == 'maf_selector'</filter> + </data> + <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)"> + <filter>export_select['format'] == 'vg_selector'</filter> + </data> + <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)"> + <filter>export_select['format'] == 'ah_selector'</filter> + </data> + </outputs> + <tests> + <!-- this fails because no reference level is set --> + <test expect_failure="true"> + <conditional name="export_select"> + <param name="format" value="maf_selector"/> + </conditional> + <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals.hal"/> + </test> + <!-- within-species mode --> + <test expect_num_outputs="1"> + <conditional name="export_select"> + <param name="ref_level" value="simMouse_chr6"/> + <param name="format" value="maf_selector"/> + </conditional> + <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/> + <output name="out_maf" location="https://zenodo.org/record/8336793/files/set_reference.maf"/> + </test> + <!-- between-species --> + <test expect_num_outputs="1"> + <conditional name="export_select"> + <param name="ref_level" value="simMouse_chr6"/> + <param name="format" value="maf_selector"/> + </conditional> + <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.hal"/> + <output name="out_maf" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.maf"/> + </test> + <!-- assembly hub format --> + <test expect_num_outputs="1"> + <conditional name="export_select"> + <param name="format" value="ah_selector"/> + </conditional> + <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/> + <output name="out_ah"> + <assert_contents> + <has_archive_member path="assemblyhub/hub.txt"/> + </assert_contents> + </output> + </test> + <!-- vg format --> + <test expect_num_outputs="1"> + <conditional name="export_select"> + <param name="format" value="vg_selector"/> + <param name="ref_level" value="simMouse_chr6"/> + </conditional> + <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/> + <output name="out_vg"> + <assert_contents> + <has_size value="860452" delta="200000"/> + </assert_contents> + </output> + </test> + <!-- gfa format (gfa2): not implemented --> + </tests> + <help><![CDATA[ +**What it does** + +Converts the HAL output from `Cactus whole-genome multiple sequence +aligner <root?tool_id=cactus_cactus>`__ into other formats. + +**Input** + +A `HAL +file <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__ +from `Cactus <root?tool_id=cactus_cactus>`__. + +**Output** + +Currently, you can export a pangenome in VG format, for use with +`vg <https://github.com/vgteam/vg>`__, or Multiple Alignment Format +(MAF). Note that these files are **reference-based**, so it will contain +alignments to a single reference from your list of inputs (i.e. not a +graph). You have to provide this with the ‘reference genome’ option. + +You can also export an Assembly Hub for use with the UCSC Genome Browser. +]]></help> + <expand macro="citations"/> +</tool>