annotate expression_get_biomaterials.xml @ 16:af64b9e6691b draft default tip

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 20d8d84d66eb27f870cadb94a02c97806090df24

<?xml version="1.0"?>
<tool id="expression_get_biomaterials" name="Chado biomaterial get" 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 get_biomaterials

#if $provider_id:
  --provider_id '$provider_id'
#end if
#if $biomaterial_id:
  --biomaterial_id '$biomaterial_id'
#end if
#if $organism_id:
  --organism_id '$organism_id'
#end if
#if $biomaterial_name:
  --biomaterial_name '$biomaterial_name'
#end if
#if $analysis_id:
  --analysis_id '$analysis_id'
#end if

| jq -S . > '$results'

@STOP_PSQL@
    ]]></command>
    <inputs>
      <expand macro="psql_target"/>
        <!-- options -->
        <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" />
        <param argument="analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" optional="true" />
        <param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" optional="true" />
        <param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial id" optional="true" />
        <param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Limit query to the selected biomaterial name" optional="true" />

        <expand macro="wait_for"/>
    </inputs>
    <outputs>
        <data format="json" name="results"/>
    </outputs>
    <help>
List biomaterials in the database

@HELP@
    </help>
</tool>