Mercurial > repos > gga > apollo_list_organism
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
author | gga |
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date | Wed, 11 Jan 2023 11:48:41 +0000 |
parents | 78abc724d792 |
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<?xml version="1.0"?> <macros> <token name="@WRAPPER_VERSION@">4.2.13+galaxy0</token> <xml name="requirements"> <requirements> <requirement type="package" version="4.2.13">apollo</requirement> <yield/> </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token> <token name="@EXT_URL@"> "\$GALAXY_WEBAPOLLO_EXT_URL" </token> <token name="@URL@"> "\$GALAXY_WEBAPOLLO_URL" </token> <token name="@AUTH@"><![CDATA[ if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then echo "__default: local" > '.auth.yml' && echo "local:" >> '.auth.yml' && echo " url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' && echo " username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' && echo " password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' && export ARROW_GLOBAL_CONFIG_PATH='.auth.yml' ; fi && ]]></token> <token name="@ORG_OR_GUESS@"> <![CDATA[ #if $org_source.source_select == "auto_json": --org_json '${org_source.org_file}' #elif $org_source.source_select == "select": --org_id '${org_source.org_select}' #else: --org_raw '${org_source.org_raw}' #end if ]]> </token> <token name="@ORG_CN_OR_GUESS@"> <![CDATA[ @ORG_OR_GUESS@ #if $cn_source.source_select == "auto": #if str($cn_source.cn_file) != "None": --seq_fasta '$cn_source.cn_file' #end if #else #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0: --seq_raw #for $item in $cn_source.refseqs: '${item.refseq}' #end for #end if #end if ]]> </token> <xml name="org_or_guess"> <conditional name="org_source"> <param name="source_select" type="select" label="Organism Common Name Source"> <option value="select">Select</option> <option value="direct">Direct Entry</option> <option value="auto_json">Autodetect from Apollo JSON</option> </param> <when value="select"> <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" /> </when> <when value="direct"> <param name="org_raw" type="text" label="Organism Common Name" optional="False" /> </when> <when value="auto_json"> <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" /> </when> </conditional> </xml> <xml name="cn_or_guess"> <expand macro="org_or_guess" /> <conditional name="cn_source"> <param name="source_select" type="select" label="Organism Sequence(s) Source"> <option value="all">All Refseqs</option> <option value="direct">Direct Entry</option> <option value="auto">Autodetect from Fasta</option> </param> <when value="all"> </when> <when value="auto"> <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/> </when> <when value="direct"> <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract"> <param name="refseq" type="text" label="Reference sequence(s)" /> </repeat> </when> </conditional> </xml> <xml name="citations"> <citations> <citation type="doi">10.1371/journal.pcbi.1006790</citation> </citations> </xml> <xml name="gff3_input"> <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> </xml> <token name="@GENOME_SELECTOR_PRE@"> #if $reference_genome.reference_genome_source == 'history': ln -s '$reference_genome.genome_fasta' genomeref.fa; #end if </token> <token name="@GENOME_SELECTOR@"> #if $reference_genome.reference_genome_source == 'cached': '${reference_genome.fasta_indexes.fields.path}' #elif $reference_genome.reference_genome_source == 'history': genomeref.fa #end if </token> <token name="@REFERENCES@"> <![CDATA[ ------ **Citation** If you use this tool in Galaxy, please cite: Helena Rasche, Anthony Bretaudeau, and Mateo Boudet (2019), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_ ]]> </token> </macros>