# HG changeset patch
# User dfornika
# Date 1548733323 18000
# Node ID 4bfeab125a687b24f562137357a86f17bfc0af98
# Parent  033da434cfaf0f2015ac116511d6a876a26951e6
planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/mash commit d16df8c9ded906bec52edc3cbfa5a91a5573d009-dirty

diff -r 033da434cfaf -r 4bfeab125a68 mash_dist.xml
--- a/mash_dist.xml	Mon Jan 28 22:00:44 2019 -0500
+++ b/mash_dist.xml	Mon Jan 28 22:42:03 2019 -0500
@@ -9,24 +9,24 @@
     <version_command>mash --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         #if str( $query_input.query_input_selector ) == "single"
-          #set $query $query_input.query.element_identifier
-          ln -s '$query_input.query' '$query' &&
+          #set $query = $query_input.query.element_identifier
+          cat '$query_input.query' > '$query' &&
         #end if
         #if str( $query_input.query_input_selector ) == "paired"
-        #set $query $query_input.query_1.element_identifier
+        #set $query = $query_input.query_1.element_identifier
           cat '$query_input.query_1' '$query_input.query_2' > '$query' && 
         #end if
         #if str( $query_input.query_input_selector ) == "paired_collection"
-          #set $query $query_input.query.element_identifier
+          #set $query = $query_input.query.element_identifier
           cat '$query_input.query.forward' '$query_input.query.reverse' > '$query' &&
         #end if
         #if str( $query_input.query_input_selector ) == "collection"
+	  #set $query = $query_input.query.element_identifier
           cat '${ str($query_input.query).replace(',', '\' \'') }' > '$query' &&
         #end if
+	ln -s '$reference' ref.msh &&
         mash dist
-             -i $minimum_identity_to_report
-             -v $maximum_p_value_to_report
-             '$reference'
+             'ref.msh'
              '$query'
              > '$output'
     ]]></command>
@@ -47,16 +47,12 @@
                 <param name="query" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
             </when>
 	    <when value="collection">
-                <param name="query" format="@INTYPES@" type="data_collection" collection_type="single" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+                <param name="query" format="@INTYPES@" type="data_collection" collection_type="single" label="Select a collection" help="See help section for an explanation of dataset collections"/>
             </when>
             <when value="paired_collection">
                 <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 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."/>
     </inputs>
     <outputs>
         <data name="output" format="tabular" />
@@ -72,7 +68,7 @@
             <param name="reference" value="NZ_MYON01000010.1.msh"/>
 	    <param name="query_input_selector" value="single"/>
             <param name="query" value="ERR024951_seqtk_sample_1000_2.fastq"/>
-            <output name="output" file="mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
+            <output name="output" file="mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
         </test>
         <test>
             <param name="reference" value="NZ_MYON01000010.1.msh"/>
diff -r 033da434cfaf -r 4bfeab125a68 test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv
--- a/test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv	Mon Jan 28 22:00:44 2019 -0500
+++ b/test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv	Mon Jan 28 22:42:03 2019 -0500
@@ -1,1 +1,1 @@
-NZ_MYON01000010.1.fa	test-data/ERR024951_seqtk_sample_1000_1.fastq	0.263022	6.65616e-11	2/1000
+NZ_MYON01000010.1.fa	ERR024951_seqtk_sample_1000_1.fastq	0.263022	6.65616e-11	2/1000
diff -r 033da434cfaf -r 4bfeab125a68 test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv
--- a/test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv	Mon Jan 28 22:00:44 2019 -0500
+++ b/test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv	Mon Jan 28 22:42:03 2019 -0500
@@ -1,1 +1,1 @@
-NZ_MYON01000010.1.fa	reads.fastq	0.210897	3.7103e-32	6/1000
+NZ_MYON01000010.1.fa	ERR024951_seqtk_sample_1000_1.fastq	0.210897	3.7103e-32	6/1000
diff -r 033da434cfaf -r 4bfeab125a68 test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv
--- a/test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv	Mon Jan 28 22:00:44 2019 -0500
+++ b/test-data/mash_dist_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv	Mon Jan 28 22:42:03 2019 -0500
@@ -1,1 +1,1 @@
-NZ_MYON01000010.1.fa	test-data/ERR024951_seqtk_sample_1000_2.fastq	0.219531	1.69119e-27	5/1000
+NZ_MYON01000010.1.fa	ERR024951_seqtk_sample_1000_2.fastq	0.219531	1.69119e-27	5/1000