# HG changeset patch
# User dfornika
# Date 1582577782 0
# Node ID 561dc2d84650a87af74fd8598eb095bf74d361e1
# Parent  7eed09e9dabe5650f663e820a494bc3708068b25
Uploaded

diff -r 7eed09e9dabe -r 561dc2d84650 mash_screen.xml
--- a/mash_screen.xml	Mon Feb 24 20:55:48 2020 +0000
+++ b/mash_screen.xml	Mon Feb 24 20:56:22 2020 +0000
@@ -1,14 +1,16 @@
-<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy1" profile="19.01">
-    <description>determines how well query sequences are contained within a pool of sequences.</description>
+<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy2" profile="19.01">
+    <description>determines how well query sequences are contained within a pool of sequences</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
-    </requirements>
-    <version_command>mash --version</version_command>
+    <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
@@ -43,28 +45,45 @@
                 <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" />
-        <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/>
-        <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." />
-        <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/>
+        <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" />
+        <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
     </inputs>
     <outputs>
         <data name="output" format="tabular" />
     </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_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_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"/>
@@ -73,7 +92,8 @@
         </test>
     </tests>
     <help><![CDATA[
-Description:
+
+**What it does**
 
   Determine how well query sequences are contained within a pool of sequences.
   The queries must be formatted as a single Mash sketch file (.msh), created
@@ -85,18 +105,5 @@
   query-comment], where median-multiplicity is computed for shared hashes, based
   on the number of observations of those hashes within the pool.
   ]]></help>
-    <citations>
-        <citation type="bibtex">
-@article{ondov2016mash,
-  title={Mash: fast genome and metagenome distance estimation using MinHash},
-  author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
-  journal={Genome biology},
-  volume={17},
-  number={1},
-  pages={132},
-  year={2016},
-  publisher={BioMed Central}
-  }
-        </citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>