diff mash_sketch.xml @ 0:68084b06ae83 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mash_sketch.xml	Sun Feb 16 17:03:04 2020 -0500
@@ -0,0 +1,97 @@
+<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01">
+    <description>
+        Create a reduced representation of a sequence or set of sequences, based on min-hashes
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        mash sketch
+            -s '${sketch_size}'
+            -k '${kmer_size}'
+            #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
+              -m '${reads_assembly.minimum_kmer_copies}'
+              -r
+              #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
+                '$reads_assembly.reads_input.reads_1' '$reads_assembly.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 ( $reads_assembly.reads_assembly_selector ) == "assembly"
+              -p \${GALAXY_SLOTS:-1}
+              '${assembly}'
+              ${reads_assembly.individual_sequences}
+            #end if
+            -o 'sketch'
+    ]]></command>
+    <inputs>
+        <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="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>
+                <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000" label="Minimum copies of each k-mer required to pass noise filter"/>
+            </when>
+            <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" label="Sketch size" />
+        <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32" label="kmer size" />
+    </inputs>
+    <outputs>
+        <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads_assembly_selector" value="reads" />
+            <param name="reads_input_selector" value="single"/>
+            <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+            <output name="sketch" file="ERR024951_seqtk_sample_1000_1.sketch.msh" compare="sim_size" />
+        </test>
+        <test>
+            <param name="reads_assembly_selector" value="assembly" />
+            <param name="assembly" value="test_assembly.fasta"/>
+            <output name="sketch" file="test_assembly.sketch.msh" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+  Create a sketch file, which is a reduced representation of a sequence or set
+  of sequences (based on min-hashes) that can be used for fast distance
+  estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can
+  be given to read from standard input. Input files can also be files of file
+  names (see -l). For output, one sketch file will be generated, but it can have
+  multiple sketches within it, divided by sequences or files (see -i). By
+  default, the output file name will be the first input file with a '.msh'
+  extension, or 'stdin.msh' if standard input is used (see -o).
+  ]]></help>
+    <expand macro="citations"/>
+</tool>