Mercurial > repos > gga > apollo_export
diff macros.xml @ 0:b4a85d0c85b8 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:47:07 -0400 |
parents | |
children | 5559e41721c3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 11 05:47:07 2017 -0400 @@ -0,0 +1,129 @@ +<?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="0.16.0">future</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>