Mercurial > repos > gga > apollo_list_organism
view macros.xml @ 8:2c749ed310da draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 2488ac4ea447c45886ce5c7b102fb28c5839d26b
author | gga |
---|---|
date | Wed, 10 Apr 2019 14:07:45 -0400 |
parents | b69804a685e2 |
children | f26ac3b582e1 |
line wrap: on
line source
<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.65">biopython</requirement> <requirement type="package" version="0.6.2">bcbiogff</requirement> <requirement type="package" version="2.12.4">requests</requirement> <requirement type="package" version="1.11.0">six</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="@ADMIN_AUTH@"> "\$GALAXY_WEBAPOLLO_URL" "\$GALAXY_WEBAPOLLO_USER" "\$GALAXY_WEBAPOLLO_PASSWORD" </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="test_result"> <assert_stderr> <has_text text="MissingSchema" /> </assert_stderr> </xml> <xml name="citations"> <citations> </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: Eric Rasche (2016), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_ ]]> </token> </macros>