diff data_manager/fetch_refseq.xml @ 19:d118e256faca draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"

--- a/data_manager/fetch_refseq.xml	Fri Sep 28 23:46:24 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.19" tool_type="manage_data">
-    <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description>
-    <requirements>
-        <requirement type="package" version="3">python</requirement>
-    </requirements>
-    <command detect_errors="aggressive"><![CDATA[
-    python3 $__tool_directory__/fetch_refseq.py
-      #if str( $advanced.advanced_selector ) == 'advanced':
-        '${advanced.compress}'
-      #end if
-      --galaxy_datamanager_filename '${output_file}'
-      --division_names ${division_names}
-      --mol_types ${mol_types}
-      #if str( $pin_date ) != 'NO':
-        --pin_date '${pin_date}'
-      #end if
-    ]]></command>
-    <inputs>
-        <param argument="division_names" type="select" label="RefSeq division" multiple="true">
-            <option value="archea">Archea</option>
-            <option value="bacteria">Bacteria</option>
-            <option value="complete">Complete</option>
-            <option value="fungi">Fungi</option>
-            <option value="invertebrate">Invertebrate</option>
-            <option value="mitochondrion">Mitochondrion</option>
-            <option value="other">Other</option>
-            <option value="plant">Plant</option>
-            <option value="plasmid">Plasmid</option>
-            <option value="plastid">Plastid</option>
-            <option value="protozoa">Protozoa</option>
-            <option value="vertebrate_mammalian">Mammalian Vertebrate</option>
-            <option value="vertebrate_other">Other Vertebrate</option>
-            <option value="viral">Viral</option>
-        </param>
-        <param argument="mol_types" type="select" multiple="true" label="Molecule type" help="Select at least one of genomic, protein or rna sequence">
-            <option value="protein">Protein</option>
-            <option value="genomic">Genomic (DNA)</option>
-            <option value="rna">RNA</option>
-        </param>
-        <conditional name="advanced">
-            <param name="advanced_selector" type="select" label="Advanced Options">
-                <option value="basic" selected="True">Basic</option>
-                <option value="advanced">Advanced</option>
-            </param>
-            <when value="basic">
-            </when>
-            <when value="advanced">
-                <param type="boolean" argument="--compress" truevalue="--compress" falsevalue="" label="Compress FASTA files" 
-                    help="Compress downloaded FASTA files (with gzip). Limits compatibility with tools expecting uncompressed FASTA."/>
-            </when>
-        </conditional>
-        <param argument="--pin_date" type="hidden" value="NO" help="Used for testing"/>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="data_manager_json"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="division_names" value="plastid"/>
-            <param name="mol_types" value="protein"/>
-            <param name="pin_date" value="2018-03-14"/>            
-            <param name="advanced_selector" value="basic"/>
-            <output name="output_file">
-                <assert_contents>
-                    <has_text text="2018-03-14"/>
-                    <has_text text="refseq_plastid"/>
-                    <has_text text="/refseq_plastid."/>
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help><![CDATA[
-This data manager fetches FASTA format collections of proteins, nucleotides (genomic DNA) and RNA
-from NCBI's RefSeq_ data collection.
-
-RefSeq is released every two months and consists of a number of divisions. Some sequences are shared
-between multiple divisions. This data manager allows the Galaxy administrator to select which
-divisions and which molecule types within each division to download. Once downloaded the
-files are made accessible by adding an entry into the *all_fasta* data table.
-
-.. _RefSeq: https://www.ncbi.nlm.nih.gov/refseq/
-    ]]>
-    </help>
-    <citations>
-        <citation type="doi">10.1093/nar/gkv1189</citation>
-    </citations>
-</tool>
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