Mercurial > repos > dfornika > mash

changeset 1:0d11360e6194 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 03b0ce2da0b398127862d5d235bed8f9c0b23622-dirty
author dfornika
date Tue, 22 Jan 2019 16:47:04 -0500
parents 55fdc6724f03
children 74242e18b66a
files mash_screen.xml
diffstat 1 files changed, 31 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/mash_screen.xml	Wed Jan 09 18:30:35 2019 -0500
+++ b/mash_screen.xml	Tue Jan 22 16:47:04 2019 -0500
@@ -14,12 +14,36 @@
              -i $minimum_identity_to_report
              -v $maximum_p_value_to_report
              queries.msh
-             '${ str($pool).replace(',', '\' \'') }'
+	     #if str( $pool.pool_input_selector ) == "paired"
+               '$pool.pool_1' '$pool.pool_2'
+             #end if
+             #if str( $pool.pool_input_selector ) == "paired_collection"
+               '$pool.pool.forward' '$pool.pool.reverse'
+             #end if
+             #if str( $fastq_input.fastq_input_selector ) == "single"
+               '$pool.pool'
+             #end if
              > '$output'
     ]]></command>
     <inputs>
+        <conditional name="pool">
+	    <param name="pool_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
+		<option value="paired">Paired</option>
+		<option value="single">Single</option>
+		<option value="paired_collection">Paired Collection</option>
+	    </param>
+	    <when value="paired">
+		<param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
+		<param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+	    </when>
+	    <when value="single">
+		<param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
+	    </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 name="queries" type="data" format="binary" />
-        <param type="data" multiple="true" name="pool" format="@INTYPES@" />
         <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."/>
@@ -30,17 +54,21 @@
     <tests>
         <test>
             <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="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" value="NZ_MYON01000010.1.msh"/>
-            <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq,ERR024951_seqtk_sample_1000_2.fastq"/>
+	    <param name="pool_selector" value="paired"/>
+            <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+	    <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
         </test>
     </tests>