annotate expression_add_biomaterial.xml @ 8:8904dc99a492 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bfca9a8c38694bbf04d92a6668e4ea31cf658eb8"

<?xml version="1.0"?>
<tool id="expression_add_biomaterial" name="Chado biomaterial add" version="@WRAPPER_VERSION@">
    <description></description>
	<macros>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements"/>
    <code file="chado.py"/>
	<command detect_errors="aggressive"><![CDATA[
@START_PSQL@ &&

chakin expression add_biomaterial

#if $description:
  --description '$description'
#end if
#if $biomaterial_provider:
  --biomaterial_provider '$biomaterial_provider'
#end if
#if $biosample_accession:
  --biosample_accession '$biosample_accession'
#end if
#if $sra_accession:
  --sra_accession '$sra_accession'
#end if
#if $bioproject_accession:
  --bioproject_accession '$bioproject_accession'
#end if
#if $attributes:
  --attributes '$attributes'
#end if

'$biomaterial_name'
'$organism_id'

| jq -S . > '$results'

@ZIP_PSQL@
    ]]></command>
	<inputs>
    <expand macro="psql_target"/>
	    <!-- arguments -->
		<param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Biomaterial name" />
		<param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />

	    <!-- options -->
		<param name="description" label="Description" argument="--description" type="text" help="Description of the biomaterial" optional="true" />
		<param name="biomaterial_provider" label="Biomaterial Provider" argument="--biomaterial_provider" type="text" help="Biomaterial provider name" optional="true" />
		<param name="biosample_accession" label="Biosample Accession" argument="--biosample_accession" type="text" help="Biosample accession number" optional="true" />
		<param name="sra_accession" label="Sra Accession" argument="--sra_accession" type="text" help="SRA accession number" optional="true" />
		<param name="bioproject_accession" label="Bioproject Accession" argument="--bioproject_accession" type="text" help="Bioproject accession number" optional="true" />
		<param name="attributes" label="Attributes" argument="--attributes" type="data" format="json" help="Custom attributes (In JSON dict form)" optional="true" />

		<expand macro="wait_for"/>

	</inputs>
	<outputs>
		<data format="json" name="results"/>
		<data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} '${biomaterial_name}' on ${on_string}">
			<filter>psql_target['method'] == "pgtools"</filter>
		</data>
	</outputs>
	<help>
Add a new biomaterial to the database

@HELP@
	</help>
</tool>