changeset 9:31dd7ace2be4 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 90c51a29d5aaab3f8dea67ac12098dc386e23b4e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Nov 05 08:44:11 2015 -0500
@@ -0,0 +1,64 @@
+Galaxy wrapper for MetaPhlAn2
+=============================
+
+MetaPhlAn is a computational tool for profiling the composition of microbial 
+communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun 
+sequencing data with species level resolution. For more information, check the 
+[user manual](https://bitbucket.org/biobakery/metaphlan2)
+
+# Installation
+
+## Automated installation
+
+On a Galaxy instance, the wrapper can be automatically installed using the 
+ToolShed. This will automatically install the dependencies, configure the Galaxy
+instance for the tool and data, ...
+
+## Manual installation
+
+For manual installation, the files `metaphlan2.xml` must be put in the `tools/metaphlan2/`
+ folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as 
+normal:
+
+```
+<section name="Profile microbial community composition" id="metaphlan2">
+    <tool file="metaphlan2/metaphlan2.xml" />
+</section>
+```
+
+MetaPhlAn2 must be installed somewhere on the system path. It can be done using:
+
+```
+planemo dependency_script ~/repositories/galaxytools/tools/metaphlan2/
+bash dep_install.sh
+source env.sh
+```
+
+To test the Galaxy integration, the functional tests can be runned:
+
+```
+./run_tests.sh -sid metaphlan2
+```
+
+# Bug Reports
+
+Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
+
+# Developers
+
+A release can be pushed to the test or main "Galaxy Tool Shed", using the following 
+Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
+
+```
+planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/metaphlan2/
+```
+
+or:
+
+```
+planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/metaphlan2/
+```
+
+# License (Apache 2) 
+
+This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details
\ No newline at end of file

--- a/metaphlan2.xml	Wed Oct 28 12:41:43 2015 -0400
+++ b/metaphlan2.xml	Thu Nov 05 08:44:11 2015 -0500
@@ -105,28 +105,28 @@
 
         <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
 
-        <param name="bowtie2_output" type='boolean' checked="true" truevalue='' falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
-        <param name="sam_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a sam file?" help="" />
-        <param name="biom_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a biom file?" help="" />
+        <param name="bowtie2_output" type='boolean' checked="true" truevalue="" falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
+        <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
+        <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
     </inputs>
 
     <outputs>
-        <data format_source="txt" name="output_file" 
+        <data format="txt" name="output_file" 
             metadata="input_sequence_file" 
             label="Profile of communities on ${on_string} (MetaPhlAn)" />
 
-        <data format_source="bowtie2" name="bowtie2_output_file" 
+        <data format="bowtie2" name="bowtie2_output_file" 
             metadata="input_sequence_file" 
             label="Bowtie2 output on ${on_string} (MetaPhlAn)">
-            <filter>!bowtie2_output</filter>
+            <filter>bowtie2_output != '--no_map' </filter>
         </data>
 
-        <data format_source="sam" name="sam_output_file" 
+        <data format="sam" name="sam_output_file" 
             metadata="input_sequence_file" 
             label="Sam output on ${on_string} (MetaPhlAn)">
             <filter>sam_output</filter>
         </data>
-        <data format_source="biom" name="biom_output_file" 
+        <data format="biom" name="biom_output_file" 
             metadata="input_sequence_file" 
             label="Biom output on ${on_string} (MetaPhlAn)">
             <filter>biom_output</filter>
@@ -136,6 +136,18 @@
     <tests>
         <test>
             <param name="input_file" value="input_sequences.fastq"/>
+            <param name="analysis_type_select" value="rel_ab" />
+            <param name="taxonomic_level" value="a" />
+            <param name="min_cu_len" value="2000" />
+            <param name="min_alignment_len" value="0" />
+            <param name="ignore_viruses" value="" />
+            <param name="ignore_eukaryotes" value="" />
+            <param name="ignore_bacteria" value="" />
+            <param name="ignore_archaea" value="" />
+            <param name="stat_q" value="0.1" />
+            <param name="bowtie2_output" value='--no_map' />
+            <param name="sam_output" value='False' />
+            <param name="biom_output" value='False' />
             <output name="output_file" file="profiled_metagenome.txt"/>
         </test>
     </tests>