# HG changeset patch
# User dfornika
# Date 1581631820 0
# Node ID 13516965dc5960b0d2c48114fa267c754341f984
# Parent  3a8ef132023c5ab988f11e2b86684ea5ab3c2ff6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit d12104bf41c388c45b1188c55928c9e678063bc7-dirty"

diff -r 3a8ef132023c -r 13516965dc59 mash_sketch.xml
--- a/mash_sketch.xml	Thu Feb 13 20:25:09 2020 +0000
+++ b/mash_sketch.xml	Thu Feb 13 22:10:20 2020 +0000
@@ -11,37 +11,54 @@
     <version_command>mash --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         mash sketch
-             -s '${sketch_size}'
-             -k '${kmer_size}'
-             -m '${minimum_kmer_copies}'
-             -r       
-             #if str( $input.input_selector ) == "paired"
-               '$input.reads_1' '$input.reads_2'
-             #end if
-             #if str( $input.input_selector ) == "paired_collection"
-               '$input.reads.forward' '$input.reads.reverse'
-             #end if
-             #if str( $input.input_selector ) == "single"
-               '$input.reads'
-             #end if
-             -o 'sketch'
+            -s '${sketch_size}'
+            -k '${kmer_size}'
+            -m '${minimum_kmer_copies}'
+            #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
+              -r
+              #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
+                '$reads_input.reads_1' '$reads_input.reads_2'
+              #end if
+              #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"
+                '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse'
+              #end if
+              #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"
+                '$reads_assembly.reads_input.reads'
+              #end if
+            #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"
+              '${assembly}'
+              ${reads_assembly.individual_sequences}
+            #end if
+            -o 'sketch'
     ]]></command>
     <inputs>
-        <conditional name="input">
-            <param name="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>
+        <conditional name="reads_assembly">
+            <param name="reads_assembly_selector" type="select" label="Input: Reads or Assemblies">
+                <option selected="True" value="reads">Reads</option>
+                <option value="assembly">Assembly</option>
             </param>
-            <when value="paired">
-                <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
-                <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+            <when value="reads">
+                <conditional name="reads_input">
+                    <param name="reads_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="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
+                        <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+                    </when>
+                    <when value="single">
+                        <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
+                    </when>
+                    <when value="paired_collection">
+                        <param name="reads" 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>
             </when>
-            <when value="single">
-                <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
-            </when>
-            <when value="paired_collection">
-                <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+            <when value="assembly">
+                <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
+                <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/> 
             </when>
         </conditional>
         <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" />
@@ -53,10 +70,16 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_selector" value="single"/>
+            <param name="reads_assembly_selector" value="reads" />
+            <param name="reads_input_selector" value="single"/>
             <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
             <assert_stderr has_text="Estimated genome size:"/>
         </test>
+        <test>
+            <param name="reads_assembly_selector" value="assembly" />
+            <param name="assembly" value="test_assembly.fasta"/>
+            <assert_stderr has_text="Sketching"/>
+        </test>
     </tests>
     <help><![CDATA[
 Description:
diff -r 3a8ef132023c -r 13516965dc59 test-data/test_assembly.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_assembly.fasta	Thu Feb 13 22:10:20 2020 +0000
@@ -0,0 +1,3 @@
+>test
+GCATGTCGATCTGTGTGCTAGTCGTAGTCGATCGATCTGATCGATCTGTCAGTCAGTAGT
+CTCAGCGATGCATTATTATATTATATTATCGATCGATGCTGATCGATTATATTCGATCTG