# HG changeset patch
# User iuc
# Date 1504082971 14400
# Node ID 76c040c8b9fc361af019466ba2b1fb8daebc14f9
# Parent  6273e2721fa33ac6a0dea71cef27748bc36669a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3

diff -r 6273e2721fa3 -r 76c040c8b9fc README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Aug 30 04:49:31 2017 -0400
@@ -0,0 +1,34 @@
+## PICRUSt Galaxy Wrapper
+
+This page is for anyone interested in installing [PICRUSt](http://picrust.github.io/picrust/) in a [galaxy instance](https://galaxyproject.org/).The below descriptions should clarify the most confusing part of the installation.
+
+The most important steps are that you need to go to the Galaxy IUC tool shed and install the 4 wrapper scripts there along with PICRUSt itself. If you install PICRUSt through this interface the precalculated files will not also be installed, you will need to download them separately (see below).
+
+Once these scripts are installed sections like the one below should be added to *galaxy/config/shed_tool_data_table_conf.xml* automatically. They will point to different *picrust_precalculated.loc* files; you only need to edit one of them since all of these files will be checked.
+
+```
+<tables>
+    <table name="picrust_precalculated" comment_char="#">
+        <columns>name, value</columns>
+        <file path="tool-data/picrust_precalculated.loc" />
+    </table>
+</tables>
+```
+
+You should download the precalculated files from http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/.
+
+Most users only use the below two files (however you can also download the precalculated COG and RFAM abundances):
+```
+16S_13_5_precalculated.tab.gz
+ko_13_5_precalculated.tab.gz
+```
+
+Once you download these files we just need to point to them in a *picrust_precalculated.loc* file.
+
+An example file is shown below. Note that tabs should separate the two columns and that in the below command "16S 13_5" (separated by one space) is one example dbname.
+
+```
+<dbname>       <file_base>
+16S 13_5    /path/to/16S_13_5_precalculated.tab.gz
+ko 13_5    /path/to/ko_13_5_precalculated.tab.gz
+```
diff -r 6273e2721fa3 -r 76c040c8b9fc macros.xml
--- a/macros.xml	Thu Dec 08 06:28:17 2016 -0500
+++ b/macros.xml	Wed Aug 30 04:49:31 2017 -0400
@@ -1,8 +1,8 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">1.0.1</token>
+    <token name="@WRAPPER_VERSION@">1.1.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.0.1">picrust</requirement>
+            <requirement type="package" version="1.1.1">picrust</requirement>
         </requirements>
     </xml>
 
@@ -31,8 +31,15 @@
 
     <xml name="biom_format_select">
         <param name="output_type" type="select" label="Format of the output BIOM file">
-            <option value="json" selected="true">JSON</option>
-            <option value="hdf5">HDF5</option>
+            <option value="hdf5" selected="true">HDF5</option>
+            <option value="json">JSON</option>
+            <option value="tsv">Classic (tab-separated text)</option>
+        </param>
+    </xml>
+
+    <xml name="biom_format_select_no_json">
+        <param name="output_type" type="select" label="Format of the output BIOM file">
+            <option value="hdf5" selected="true">HDF5</option>
             <option value="tsv">Classic (tab-separated text)</option>
         </param>
     </xml>
@@ -40,20 +47,20 @@
     <xml name="biom_output">
         <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
             <change_format>
-                <when input="output_type" value="json" format="json"/>
+                <when input="output_type" value="json" format="biom1"/>
                 <when input="output_type" value="tsv" format="tabular"/>
-                <when input="output_type" value="hdf5" format="hdf5"/>
+                <when input="output_type" value="hdf5" format="h5"/>
             </change_format>
         </data>
     </xml>
 
     <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
-        #if $output_type == "json":
-            && biom convert -i tempbiom -o '$out_biom' --to-json
+        #if $output_type == "hdf5":
+            && mv tempbiom '$out_biom'
         #elif $output_type == "tsv":
             && biom convert -i tempbiom -o '$out_biom' --to-tsv
-        #else
-            && biom convert -i tempbiom -o '$out_biom' --to-hdf5
+        #else:
+            && biom convert -i tempbiom -o '$out_biom' --to-json
         #end if
     ]]></token>
 
@@ -69,13 +76,13 @@
 
 For more information please visit:
 
-- Picrust Documentation: https://picrust.github.io/picrust/
-- Picrust GitHub: http://picrust.github.com/
-- Picrust Support: https://groups.google.com/d/forum/picrust-users
+- PICRUSt Documentation: https://picrust.github.io/picrust/
+- PICRUSt GitHub: http://picrust.github.com/
+- PICRUSt Support: https://groups.google.com/d/forum/picrust-users
 
 **Reference Data**
 
-Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/
+Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/
 
 ]]>
     </token>
diff -r 6273e2721fa3 -r 76c040c8b9fc normalize_by_copy_number.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalize_by_copy_number.xml	Wed Aug 30 04:49:31 2017 -0400
@@ -0,0 +1,63 @@
+<tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0">
+    <description>the relative abundance of each OTU by the predicted number of 16S copies</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        normalize_by_copy_number.py
+            -i '$input_data'
+            -o tempbiom
+            -c '$gg.precalc'
+
+            @OUTPUT_CONVERSION_COMMANDS@
+    ]]></command>
+    <inputs>
+        <param name="input_data" type="data" format="biom1,h5" label="Input file" help="biom file"/>
+        <expand macro="otu-reference-precalculated"/>
+        <expand macro="biom_format_select"/>
+    </inputs>
+    <outputs>
+        <expand macro="biom_output"/>
+    </outputs>
+    <tests>
+        <test> <!-- test with biom input -->
+            <param name="input_data" value="closed_picked_otus.biom"/>
+            <param name="source" value="hist"/>
+            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
+            <param name="output_type" value="json"/>
+            <output name="out_biom" ftype="biom1">
+                <assert_contents>
+                    <has_text text="Biological Observation Matrix"/>
+                    <has_text text="generated_by"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test> <!-- test with QIIME input and classic output -->
+            <param name="input_data" value="closed_picked_otus.tab"/>
+            <param name="source" value="hist"/>
+            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
+            <param name="output_type" value="tsv"/>
+            <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+@PICRUST_OVERVIEW@
+
+**Command Documenation**
+
+This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.
+
+Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_.
+A sample file can be downloaded here_
+
+Make sure that you specify an appropriate 16S database for this command (usually 16S 13_5).
+
+.. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html
+.. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
diff -r 6273e2721fa3 -r 76c040c8b9fc normalize_by_copynumber.xml
--- a/normalize_by_copynumber.xml	Thu Dec 08 06:28:17 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-<tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0">
-    <description>OTUs by copy number</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
-        normalize_by_copy_number.py
-            -i '$input_data'
-            -o tempbiom
-            -c '$gg.precalc'
-
-            @OUTPUT_CONVERSION_COMMANDS@
-    ]]></command>
-    <inputs>
-        <param name="input_data" type="data" format="tabular,biom1" label="Input file" help="biom file or legacy QIIME OTU table"/>
-        <expand macro="otu-reference-precalculated"/>
-        <expand macro="biom_format_select"/>
-    </inputs>
-    <outputs>
-        <expand macro="biom_output"/>
-    </outputs>
-    <tests>
-        <test> <!-- test with biom input -->
-            <param name="input_data" value="closed_picked_otus.biom"/>
-            <param name="source" value="hist"/>
-            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
-            <param name="output_type" value="json"/>
-            <output name="out_biom" ftype="json">
-                <assert_contents>
-                    <has_text text="Biological Observation Matrix"/>
-                    <has_text text="generated_by"/>
-                </assert_contents>
-            </output>
-        </test>
-        <test> <!-- test with QIIME input and classic output -->
-            <param name="input_data" value="closed_picked_otus.tab"/>
-            <param name="source" value="hist"/>
-            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
-            <param name="output_type" value="tsv"/>
-            <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/>
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-@PICRUST_OVERVIEW@
-
-**Command Documenation**
-
-This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.
-
-Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_.
-A sample file can be downloaded here_
-
-.. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html
-.. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab
-]]>
-    </help>
-    <expand macro="citations"/>
-</tool>
diff -r 6273e2721fa3 -r 76c040c8b9fc tool-data/picrust_precalculated.loc.sample
--- a/tool-data/picrust_precalculated.loc.sample	Thu Dec 08 06:28:17 2016 -0500
+++ b/tool-data/picrust_precalculated.loc.sample	Wed Aug 30 04:49:31 2017 -0400
@@ -1,6 +1,6 @@
 #This is a sample file distributed with Galaxy.
 #
-# PICRUSt supplied files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/
+# PICRUSt supplied files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/
 #
 # files may be in gzipped format or unzipped
 #
@@ -8,3 +8,4 @@
 #16S 13_5	/path/to/file/16S_13_5_precalculated.tab.gz
 #cog 13_5	/path/to/file/cog_13_5_precalculated.tab
 #ko 13_5	/path/to/file/ko_13_5_precalculated.tab.gz
+#rfam 13_5	/path/to/file/rfam_13_5_precalculated.tab.gz