Mercurial > repos > dfornika > mash_sketch

changeset 8:56c1b5f9f8bf draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit e7ac80b7bf62e50eb537b5adbe0a5ece8c4e77df-dirty"
author dfornika
date Mon, 24 Feb 2020 20:42:30 +0000
parents c4182a046647
children
files macros.xml mash_sketch.xml test-data/sketch.msh
diffstat 3 files changed, 25 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Feb 14 21:24:09 2020 +0000
+++ b/macros.xml	Mon Feb 24 20:42:30 2020 +0000
@@ -3,4 +3,21 @@
     <token name="@INTYPES@">
         fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz
     </token>
+    
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-016-0997-x</citation>
+        </citations>
+    </xml>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command>mash --version</version_command>
+    </xml>
+
 </macros>
--- a/mash_sketch.xml	Fri Feb 14 21:24:09 2020 +0000
+++ b/mash_sketch.xml	Mon Feb 24 20:42:30 2020 +0000
@@ -1,14 +1,12 @@
 <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.
+        Create a reduced representation of a sequence or set of sequences, based on min-hashes
     </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[
         mash sketch
             -s '${sketch_size}'
@@ -63,8 +61,8 @@
                 <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" />
-        <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32"/>
+        <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"/>
@@ -83,7 +81,8 @@
         </test>
     </tests>
     <help><![CDATA[
-Description:
+
+**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
@@ -94,18 +93,5 @@
   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>
-    <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>
Binary file test-data/sketch.msh has changed