Mercurial > repos > iuc > circos
diff circos.xml @ 13:c4bde687c846 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
| author | iuc |
|---|---|
| date | Wed, 12 Apr 2023 15:09:05 +0000 |
| parents | 290a11559985 |
| children |
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--- a/circos.xml Mon Nov 22 12:23:12 2021 +0000 +++ b/circos.xml Wed Apr 12 15:09:05 2023 +0000 @@ -1,11 +1,6 @@ <?xml version="1.0"?> -<tool id="circos" name="Circos" version="@WRAPPER_VERSION@"> +<tool id="circos" name="Circos" version="@WRAPPER_VERSION@" profile="21.09"> <description>visualizes data in a circular layout</description> - <xrefs> - <xref type="bio.tools">galactic_circos</xref> - <!--<xref type="bioconda">circos</xref>--> - <!--<xref type="rrid">RRID:SCR_018207</xref>--> - </xrefs> <macros> <import>macros.xml</import> <import>macros_conffiles.xml</import> @@ -18,6 +13,11 @@ <edam_operations> <edam_operation>operation_0337</edam_operation> </edam_operations> + <xrefs> + <xref type="bio.tools">galactic_circos</xref> + <!--<xref type="bioconda">circos</xref>--> + <!--<xref type="rrid">RRID:SCR_018207</xref>--> + </xrefs> <expand macro="requirements"/> <stdio> <!-- Anything other than zero is an error --> @@ -29,10 +29,10 @@ <version_command>circos --version</version_command> <command><![CDATA[ ## Directory structure -mkdir -p circos/conf/ circos/data/ && +mkdir -p circos/conf/ circos/data/; #if $reference_genome.ref.ref_source == 'history': - ln -s '$reference_genome.ref.genome_fasta' genomeref.fa && + ln -s '$reference_genome.ref.genome_fasta' genomeref.fa; #end if #if $reference_genome.ref.ref_source in ('lengths', 'cached'): @@ -48,61 +48,61 @@ <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}') #end if #end if - > circos/conf/karyotype.txt && + > circos/conf/karyotype.txt; #else if $reference_genome.ref.ref_source == 'karyotype': - cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt && + cp '${reference_genome.ref.input_karyotype}' circos/conf/karyotype.txt; #else if str($reference_genome.ref.ref_source) == 'history': ## Process the karyotype.txt file python '$__tool_directory__/karyotype-from-fasta.py' genomeref.fa - > circos/conf/karyotype.txt && + > circos/conf/karyotype.txt; #else if $reference_genome.ref.ref_source == 'preset': - cp '$__tool_directory__/karyotype/${reference_genome.ref.preset_karyotype}' circos/conf/karyotype.txt && + cp '$__tool_directory__/karyotype/${reference_genome.ref.preset_karyotype}' circos/conf/karyotype.txt; #end if python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'` - > 'circos/conf/karyotype-colors.conf' && + > 'circos/conf/karyotype-colors.conf'; -touch circos/conf/karyotype-colors.conf && +touch circos/conf/karyotype-colors.conf; ## #if $ideogram.bands.bands: ## #if $ideogram.bands.convert_bands: ## python '$__tool_directory__/process-cytogenetic-bands.py' ## '${ideogram.bands.bands}' ## >> circos/conf/karyotype.txt -## 2> circos/conf/karyotype-colors.conf && +## 2> circos/conf/karyotype-colors.conf; ## #else ## cat '${ideogram.bands.bands}' -## >> circos/conf/karyotype.txt && +## >> circos/conf/karyotype.txt; ## #end if ## #end if #if $plot_options.colour_profile: #if str($plot_options.colour_profile) == 'cg': - cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf && + cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf; #end if #end if -cp '$circos_conf' circos/conf/circos.conf && -cp '$ticks_conf' circos/conf/ticks.conf && -cp '$ideogram_conf' circos/conf/ideogram.conf && -cp '$data_conf' circos/conf/data.conf && -cp '$links_conf' circos/conf/links.conf && -cp '$test_case_conf' circos/conf/galaxy_test_case.json && +cp '$circos_conf' circos/conf/circos.conf ; +cp '$ticks_conf' circos/conf/ticks.conf ; +cp '$ideogram_conf' circos/conf/ideogram.conf ; +cp '$data_conf' circos/conf/data.conf ; +cp '$links_conf' circos/conf/links.conf ; +cp '$test_case_conf' circos/conf/galaxy_test_case.json ; ## 2D Data Plots #for $hi, $data in enumerate($sec_tdd.data): - cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt && + cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt ; #end for ## Link Tracks #for $hi, $data in enumerate($sec_links.data): - cp '${data.data_source}' circos/data/links-${hi}.txt && + cp '${data.data_source}' circos/data/links-${hi}.txt ; #end for #if $outputs.tar == "yes" - tar -czf circos.tar.gz circos && + tar -czf circos.tar.gz circos ; #end if #if $outputs.svg == "yes" or $outputs.png == "yes": @@ -617,10 +617,10 @@ </section> </inputs> <outputs> - <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot"> + <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot (PNG)"> <filter>outputs['png']</filter> </data> - <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot"> + <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot (SVG)"> <filter>outputs['svg']</filter> </data> <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files">