# HG changeset patch
# User rhpvorderman
# Date 1530630456 14400
# Node ID 9ac9089b19146cf3408fdd56c2b6ace0883cc2ce
# Parent  0a1afc109ad92894a2c5261159e2a65f2493ae2c
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 9ee0a33aa1c1e4b57b83244654f1f71a623b6247

diff -r 0a1afc109ad9 -r 9ac9089b1914 README
--- a/README	Tue Jul 03 10:29:48 2018 -0400
+++ b/README	Tue Jul 03 11:07:36 2018 -0400
@@ -1,2 +1,11 @@
-This is a fork of the data_manager_all_fasta_by_path (https://github.com/Christian-B/galaxy_shedtools/tree/master/all_fasta_by_path) data manager by Cristian-B(https://github.com/Christian-B).
-The all_fasta_by_path data manager was forked on 2017-09-07 from Christian-B's galaxy_shedtools (https://github.com/Christian-B/galaxy_shedtools) repository at commit d9f5343.
+This is a fork of the data_manager_all_fasta_by_path data manager
+by Cristian-B (https://github.com/Christian-B)
+(https://github.com/Christian-B/galaxy_shedtools/tree/master/all_fasta_by_path).
+The all_fasta_by_path data manager was forked on 2017-09-07 from
+Christian-B's galaxy_shedtools repository at commit d9f5343.
+(https://github.com/Christian-B/galaxy_shedtools).
+
+The tool has drastically changed since then, with a complete refactoring
+of the python script and the addition of unit tests for all functionality
+within the python script. A lot of indexes are now supported in addition to
+just the all_fasta one.
\ No newline at end of file
diff -r 0a1afc109ad9 -r 9ac9089b1914 data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml	Tue Jul 03 10:29:48 2018 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml	Tue Jul 03 11:07:36 2018 -0400
@@ -12,8 +12,8 @@
         --path "${path}"
         --data_table_name "${data_table}"
         --json_output_file "${json_output_file}
-        #if $data_table == "rnastar_index2"
-        --extra-columns {'with-gtf': '$data_table.with_gtf'}
+        #if $data_table_set.data_table == "rnastar_index2"
+        --extra-columns {'with-gtf': '$data_table_set.with_gtf'}
         #end if
     </command>
     <inputs>
@@ -21,28 +21,30 @@
         <param name="dbkey" type="text" value="" label="dbkey field for the entry.  Defaults to value if left blank." />
         <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." />
         <param name="path" type="text" value="" label="path field for the entry" />
-        <param name="data_table" type="select" value="" label="data table for the index">
-            <option value='all_fasta'>all_fasta</option>
-            <option value='bowtie2_indexes'>bowtie2_indexes</option>
-            <option value='bowtie_indexes'>bowtie_indexes</option>
-            <option value='bowtie_indexes_color'>bowtie_indexes_color</option>
-            <option value='bwa_mem_indexes'>bwa_mem_indexes</option>
-            <option value='bwameth_indexes'>bwameth_indexes</option>
-            <option value='fasta_indexes'>fasta_indexes</option>
-            <option value='gatk_picard_indexes'>gatk_picard_indexes</option>
-            <option value='gene_transfer'>gene_transfer</option>
-            <option value='hisat2_indexes'>hisat2_indexes</option>
-            <option value='kallisto_indexes'>kallisto_indexes</option>
-            <option value='picard_indexes'>picard_indexes</option>
-            <option value='tophat2_indexes'>tophat2_indexes</option>
-            <option value="rnastar_index2">rnastar_index2</option>
-            <when value="rnastar_index2">
-                <param name="with_gtf" type="select" value="" label="Index with embedded gtf?">
-                    <option value="0">No</option>
-                    <option value="1">Yes</option>
-                </param>
-            </when>
-        </param>
+        <conditional name="data_table_set">
+            <param name="data_table" type="select" value="" label="data table for the index">
+                <option value='all_fasta'>all_fasta</option>
+                <option value='bowtie2_indexes'>bowtie2_indexes</option>
+                <option value='bowtie_indexes'>bowtie_indexes</option>
+                <option value='bowtie_indexes_color'>bowtie_indexes_color</option>
+                <option value='bwa_mem_indexes'>bwa_mem_indexes</option>
+                <option value='bwameth_indexes'>bwameth_indexes</option>
+                <option value='fasta_indexes'>fasta_indexes</option>
+                <option value='gatk_picard_indexes'>gatk_picard_indexes</option>
+                <option value='gene_transfer'>gene_transfer</option>
+                <option value='hisat2_indexes'>hisat2_indexes</option>
+                <option value='kallisto_indexes'>kallisto_indexes</option>
+                <option value='picard_indexes'>picard_indexes</option>
+                <option value='tophat2_indexes'>tophat2_indexes</option>
+                <option value="rnastar_index2">rnastar_index2</option>
+                <when value="rnastar_index2">
+                    <param name="with_gtf" type="select" value="" label="Index with embedded gtf?">
+                        <option value="0">No</option>
+                        <option value="1">Yes</option>
+                    </param>
+                </when>
+            </param>
+        </conditional>
     </inputs>
     <outputs>
         <data name="json_output_file" format="data_manager_json"/>