diff data_manager/bowtie2_index_builder.xml @ 0:68fd790f3916 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bowtie2_index_builder.xml	Thu Apr 02 13:16:53 2020 +0000
@@ -0,0 +1,40 @@
+<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@.1+galaxy1" profile="18.09">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
+    </requirements>
+    <macros>
+        <token name="@WRAPPER_VERSION@">2.3.5</token>
+    </macros>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/bowtie2_index_builder.py'
+        '${out_file}'
+        --fasta_filename '${all_fasta_source.fields.path}'
+        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+        --fasta_description '${all_fasta_source.fields.name}'
+        --data_table_name bowtie2_indexes ${tophat2}
+    ]]></command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
+        <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <output name="out_file" value="bowtie2_data_manager.json"/>
+        </test>
+    </tests>
+
+    <help>
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+    </help>
+</tool>