changeset 3:f8e51626fc56 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit c6efcbece52dec310253537b35419839746fff7f"

--- a/mash_screen.xml	Sun Feb 16 17:03:45 2020 -0500
+++ b/mash_screen.xml	Wed Feb 26 15:49:03 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy2" profile="19.01">
+<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" profile="19.01">
     <description>determines how well query sequences are contained within a pool of sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -6,7 +6,11 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$queries' queries.msh &&
+        #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
+          ln -s '$queries_input_source.queries.fields.path' queries.msh &&
+        #elif str( $queries_input_source.queries_input_source_selector ) == 'history':
+          ln -s '$queries_input_source.queries' queries.msh &&
+        #end if
         mash screen
              $winner_takes_all
              -i $minimum_identity_to_report
@@ -41,7 +45,20 @@
                 <param name="pool" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
         </conditional>
-        <param name="queries" type="data" format="msh" />
+        <conditional name="queries_input_source">
+            <param name="queries_input_source_selector" type="select" label="Select queries from your history or use one from a tool data table?" help="">
+                <option value="tool_data_table">Queries from tool data table</option>
+                <option selected="True" value="history">Queries from history</option>
+            </param>
+            <when value="tool_data_table">
+                <param name="queries" type="select" label="Queries (Mash Sketch)">
+                    <options from_data_table="mash_sketches"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="queries" type="data" format="msh" />
+            </when>
+        </conditional>
         <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result"
             help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
         <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" />
@@ -52,18 +69,21 @@
     </outputs>
     <tests>
         <test>
+            <param name="queries_input_source_selector" value="history"/>
             <param name="queries" value="NZ_MYON01000010.1.msh"/>
             <param name="pool_input_selector" value="single"/>
             <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
         </test>
         <test>
-            <param name="queries" value="NZ_MYON01000010.1.msh"/>
+            <param name="queries_input_source_selector" value="tool_data_table"/>
+            <param name="queries" value="test_sketch"/>
             <param name="pool_input_selector" value="single"/>
             <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
         </test>
         <test>
+            <param name="queries_input_source_selector" value="history"/>
             <param name="queries" value="NZ_MYON01000010.1.msh"/>
             <param name="pool_input_selector" value="paired"/>
             <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_sketches.loc	Wed Feb 26 15:49:03 2020 -0500
@@ -0,0 +1,7 @@
+# Tab separated with three columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (path to the Mash sketch)
+#
+#
+test_sketch	"Test Sketch"	${__HERE__}/NZ_MYON01000010.1.msh

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mash_sketches.loc.sample	Wed Feb 26 15:49:03 2020 -0500
@@ -0,0 +1,7 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB, must be unique, suggest using a UUID)
+# - name (Galaxy shows this in the UI)
+# - path to sketch.msh file
+#
+# e.g.
+# 75913ffd-ed54-4691-ba75-159ab901835e<tab>Example sketch<tab>/path/to/mash_sketches/75913ffd-ed54-4691-ba75-159ab901835e/sketch.msh

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Feb 26 15:49:03 2020 -0500
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of Mash sketches in the required format -->
+    <table name="mash_sketches" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/mash_sketches.loc" />
+    </table>
+</tables>