# HG changeset patch
# User bebatut
# Date 1459409717 14400
# Node ID 7d2be77d5b83defd2bdc99a7fe45dfefa12879bc
# Parent  0d3d44f13122eaefb1a204d87af2a99450ea42a3
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty

diff -r 0d3d44f13122 -r 7d2be77d5b83 README.md
--- a/README.md	Mon Feb 22 07:09:45 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-Galaxy wrapper for HUMAnN2
-==========================
-
-HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence 
-and abundance of microbial pathways in a community from metagenomic or 
-metatranscriptomic sequencing data. For more information, check the 
-[user manual](http://huttenhower.sph.harvard.edu/humann2/manual)
-
-# 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 `humann2.xml` must be put in the `tools/humann2/`
- folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as 
-normal:
-
-```
-<section name="Profile microbial pathways in a community" id="humann2">
-    <tool file="humann2/humann2.xml" />
-</section>
-```
-
-MetaPhlAn2 must be installed somewhere on the system path. It can be done using:
-
-```
-planemo dependency_script ~/repositories/galaxytools/tools/humann2/
-bash dep_install.sh
-source env.sh
-```
-
-To test the Galaxy integration, the functional tests can be runned:
-
-```
-./run_tests.sh -sid humann2
-```
-
-# 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/humann2/
-```
-
-or:
-
-```
-planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/humann2/
-```
-
-# 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
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2.xml
--- a/humann2.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/humann2.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -1,25 +1,21 @@
-<tool id="humann2" name="HUMAnN2" version="0.1.0">
+<tool id="humann2" name="HUMAnN2" version="0.5.0">
     <description>to profile the presence/absence and abundance of microbial pathways</description>
 
-    <requirements>
-        <requirement type="package" version="2.2.5">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.7.10">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
-    \${HUMANN2_DIR}/humann2 --version
+    humann2 --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        \${HUMANN2_DIR}/humann2 
+        humann2 
             -i "$input_file"
         
             #if $taxonomic_profile.taxonomic_profile_test:
@@ -67,7 +63,7 @@
                 falsevalue='false' label="Use a custom taxonomic profile?" 
                 help="The file must have been created by MetaPhlan"/>
             <when value="true">
-                <param name="taxonomic_profile_file" type="data" format="" label="Taxonomic profile 
+                <param name="taxonomic_profile_file" type="data" format="tabular,txt" label="Taxonomic profile 
                     file" help=""/>
             </when>
             <when value="false" />
@@ -227,31 +223,31 @@
     </tests>
 
     <help><![CDATA[
-        **What it does**
+**What it does**
 
-        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
 
-        ----- 
+----- 
 
-        **Input**
+**Input**
 
-        Usually, a single file is the input. It must be one of the following types:
+Usually, a single file is the input. It must be one of the following types:
 
-            - filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format)
-            - alignment file (sam, bam or blastm8 format)
-            - gene table file (tsv or biom format)
+- filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format)
+- alignment file (sam, bam or blastm8 format)
+- gene table file (tsv or biom format)
 
-        A file with taxonomic profiles can also be given to be use to select pangenomes in ChocoPhlan database.
+A file with taxonomic profiles can also be given to be use to select pangenomes in ChocoPhlan database.
 
-        ----- 
+----- 
 
-        **Outputs**
+**Outputs**
 
-        HUMAnN creates three output files:
+HUMAnN creates three output files:
 
-            - Gene family abundance
-            - Pathway abundance
-            - Pathway coverage
+- Gene family abundance
+- Pathway abundance
+- Pathway coverage
 
     ]]></help>
 
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_join_tables.xml
--- a/humann2_join_tables.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/humann2_join_tables.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -1,20 +1,16 @@
-<tool id="humann2_join_tables" name="Join HUMAnN2 table" version="0.1.0">
+<tool id="humann2_join_tables" name="Join HUMAnN2 table" version="0.5.0">
     <description></description>
 
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
-    \${HUMANN2_DIR}/humann2_join_tables --version
+    humann2_join_tables --version
 ]]>
     </version_command>
 
@@ -27,7 +23,7 @@
         #end for
 
         && 
-        \${HUMANN2_DIR}/humann2_join_tables
+        humann2_join_tables
             -i "tmp_dir"
             -o $joined_table           
     ]]></command>
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_macros.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.2.5">bowtie2</requirement>
+            <requirement type="package" version="2.2.0">metaphlan2</requirement>
+            <requirement type="package" version="0.7.10">diamond</requirement>
+            <requirement type="package" version="0.5.0">humann2</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_merge_abundance_tables.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_merge_abundance_tables.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -0,0 +1,63 @@
+<tool id="humann2_merge_abundance_tables" name="Merge HUMAnN2 gene and pathway abundance tables" version="0.1.0">
+    <description></description>
+
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+    humann2_merge_abundance_tables --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        humann2_merge_abundance_tables
+            --input-genes $input_gene
+            --input-pathways $input_pathway
+            --gene-mapping $gene_mapping
+            --pathway-mapping $pathway-mapping
+            $remove_taxonomy
+                                  
+            -o $output_table
+    ]]></command>
+
+    <inputs>
+        <param name="input_gene" type="data" format="tsv" label="Gene family or EC 
+            abundance file" help="(--input-genes)"/>
+        <param name="input_pathway" type="data" format="tsv" label="Pathway 
+            abundance file" help="(--input-pathways)"/>
+        <param name="gene_mapping" type="data" format="tsv" label="Gene family 
+            to reaction mapping file" help="(--gene-mapping)"/>
+        <param name="pathway_mapping" type="data" format="tsv" label="Reaction to 
+            pathway mapping file" help="(--pathway-mapping)"/>
+        <param name='remove_taxonomy' type='boolean' checked="false" 
+            truevalue='--remove-taxonomy' falsevalue='' 
+            label="Remove the taxonomy from the output file?" 
+            help="(--remove-taxonomy)"/>
+        
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="output_table" label="Merged table for 
+            ${on_string} (HUMAnN2)" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        This tool merge gene and pathway abundance tables.
+
+        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_reduce_table.xml
--- a/humann2_reduce_table.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/humann2_reduce_table.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -1,25 +1,21 @@
-<tool id="humann2_reduce_table" name="Reduce HUMAnN2 table" version="0.1.0">
+<tool id="humann2_reduce_table" name="Reduce HUMAnN2 table" version="0.5.0">
     <description></description>
 
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
-    \${HUMANN2_DIR}/humann2_reduce_table --version
+    humann2_reduce_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        \${HUMANN2_DIR}/humann2_reduce_table
+        humann2_reduce_table
             -i $input_table
             -o $output_table
             --function $function
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_regroup_table.xml
--- a/humann2_regroup_table.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/humann2_regroup_table.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -1,25 +1,21 @@
-<tool id="humann2_regroup_table" name="Regroup HUMAnN2 table features" version="0.1.0">
+<tool id="humann2_regroup_table" name="Regroup HUMAnN2 table features" version="0.5.0">
     <description></description>
 
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
-    \${HUMANN2_DIR}/humann2_regroup_table --version
+    humann2_regroup_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        \${HUMANN2_DIR}/humann2_regroup_table
+        humann2_regroup_table
             -i $input_table
             -o $output_table
             --function $function
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_rename_table.xml
--- a/humann2_rename_table.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/humann2_rename_table.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -1,25 +1,21 @@
-<tool id="humann2_rename_table" name="Rename HUMAnN2 table features" version="0.1.0">
+<tool id="humann2_rename_table" name="Rename HUMAnN2 table features" version="0.5.0">
     <description></description>
 
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
-    \${HUMANN2_DIR}/humann2_rename_table --version
+    humann2_rename_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        \${HUMANN2_DIR}/humann2_rename_table
+        humann2_rename_table
             -i $input_table
             -o $output_table
 
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_renorm_table.xml
--- a/humann2_renorm_table.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/humann2_renorm_table.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -1,25 +1,21 @@
-<tool id="humann2_renorm_table" name="Renormalize HUMAnN2 table" version="0.1.0">
+<tool id="humann2_renorm_table" name="Renormalize HUMAnN2 table" version="0.5.0">
     <description></description>
 
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <version_command>
 <![CDATA[
-    \${HUMANN2_DIR}/humann2_renorm_table --version
+    humann2_renorm_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        \${HUMANN2_DIR}/humann2_renorm_table
+        humann2_renorm_table
             -i $input_table
             -o $output_table
             --norm $norm
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_rna_dna_norm.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_rna_dna_norm.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -0,0 +1,79 @@
+<tool id="humann2_rna_dna_norm" name="Combine metagenomic and metatranscriptomic HUMAnN2 data" version="0.5.0">
+    <description></description>
+
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+    humann2_rna_dna_norm --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        humann2_rna_dna_norm
+            --input_dna $input_dna
+            --input_rna $input_rna
+            --output_basename "combined"
+            $log_transform.test  
+            #if $log_transform.test:
+                --log_base $log_transform.log_base
+            #end if
+    ]]></command>
+
+    <inputs>
+        <param name="input_dna" type="data" format="tsv" label="Metagenomic table" 
+            help="(--input_dna)"/>
+        <param name="input_rna" type="data" format="tsv" label="Metatranscriptomic table" 
+            help="(--input_rna)"/>
+
+        <conditional name="log_transform">
+            <param name='test' type='boolean' checked="false" 
+                truevalue='--log_transform' falsevalue='' 
+                label="Report log-transformed relative expression values?" 
+                help="(--log_transform)"/>
+            <when value="--log_transform">
+                <param name="log_base" type="integer" min="0" max="10" value="2" 
+                    label="Base for log transformation" help="(--log_base)"/>
+            </when>
+            <when value=""/>
+        </conditional>        
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="smoothed_dna" 
+            from_work_dir="combined"
+            label="Smoothed DNA data for ${on_string} (HUMAnN2)" />
+        <data format="tsv" name="smoothed_rna" 
+            from_work_dir="combined"
+            label="Smoothed RNA data for ${on_string} (HUMAnN2)" />
+        <data format="tsv" name="normalized_rna" 
+            from_work_dir="combined"
+            label="Normalized RNA data for ${on_string} (HUMAnN2)" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        This tool normalizes combined meta'omic sequencing data. 
+
+        Given a DNA table and a RNA table, it produces smoothed RNA and DNA values as well as relative expression values. "Smoothing" means substituting a small value in place of a zero or missing value. The Witten-Bell smoothing procedure is used here.
+
+        If working with stratified data, smoothing is carried out on the stratified values and then community totals are recomputed.
+
+        The DNA and RNA columns must be 1:1 and in the same order. The units of the table should be count-like (for example, HUMAnN2 gene family abundance files).gene and pathway abundance tables.
+
+        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 0d3d44f13122 -r 7d2be77d5b83 humann2_split_table.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_split_table.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -0,0 +1,52 @@
+<tool id="humann2_split_table" name="Split HUMAnN2 table" version="0.5.0">
+    <description></description>
+
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+    humann2_split_table --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        humann2_split_table
+            -i "input_file"
+            -o "output"            
+    ]]></command>
+
+    <inputs>
+        <param name="input_file" type="data" format="tsv,biom" 
+            label="Gene/pathway table to read" help=""/>
+    </inputs>
+
+    <outputs>
+        <outputs>
+            <data format="txt" name="report">
+                <discover_datasets pattern="__designation__" ext="tabular" directory="output" visible="true" />
+            </data>
+        </outputs>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="humann2_input.fasta"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        Split HUMAnN2 table is a tool to split a gene/pathway table in table per sample.
+
+        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 0d3d44f13122 -r 7d2be77d5b83 in_development/humann2_merge_abundance_tables.xml
--- a/in_development/humann2_merge_abundance_tables.xml	Mon Feb 22 07:09:45 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-<tool id="humann2_merge_abundance_tables" name="Merge HUMAnN2 gene and pathway abundance tables" version="0.1.0">
-    <description></description>
-
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
-
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-
-    <version_command>
-<![CDATA[
-    \${HUMANN2_DIR}/humann2_merge_abundance_tables --version
-]]>
-    </version_command>
-
-    <command><![CDATA[
-        \${HUMANN2_DIR}/humann2_merge_abundance_tables
-            --input-genes $input_gene
-            --input-pathways $input_pathway
-            --gene-mapping $gene_mapping
-            --pathway-mapping $pathway-mapping
-            $remove_taxonomy
-                                  
-            -o $output_table
-    ]]></command>
-
-    <inputs>
-        <param name="input_gene" type="data" format="tsv" label="Gene family or EC 
-            abundance file" help="(--input-genes)"/>
-        <param name="input_pathway" type="data" format="tsv" label="Pathway 
-            abundance file" help="(--input-pathways)"/>
-        <param name="gene_mapping" type="data" format="tsv" label="Gene family 
-            to reaction mapping file" help="(--gene-mapping)"/>
-        <param name="pathway_mapping" type="data" format="tsv" label="Reaction to 
-            pathway mapping file" help="(--pathway-mapping)"/>
-        <param name='remove_taxonomy' type='boolean' checked="false" 
-            truevalue='--remove-taxonomy' falsevalue='' 
-            label="Remove the taxonomy from the output file?" 
-            help="(--remove-taxonomy)"/>
-        
-    </inputs>
-
-    <outputs>
-        <data format="tsv" name="output_table" label="Merged table for 
-            ${on_string} (HUMAnN2)" />
-    </outputs>
-
-    <tests>
-    </tests>
-
-    <help><![CDATA[
-        **What it does**
-
-        This tool merge gene and pathway abundance tables.
-
-        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
-
-    ]]></help>
-
-    <citations>
-    </citations>
-</tool>
\ No newline at end of file
diff -r 0d3d44f13122 -r 7d2be77d5b83 in_development/humann2_rna_dna_norm.xml
--- a/in_development/humann2_rna_dna_norm.xml	Mon Feb 22 07:09:45 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<tool id="humann2_rna_dna_norm" name="Combine metagenomic and metatranscriptomic HUMAnN2 data" version="0.1.0">
-    <description></description>
-
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
-
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-
-    <version_command>
-<![CDATA[
-    \${HUMANN2_DIR}/humann2_rna_dna_norm --version
-]]>
-    </version_command>
-
-    <command><![CDATA[
-        \${HUMANN2_DIR}/humann2_rna_dna_norm
-            --input_dna $input_dna
-            --input_rna $input_rna
-            --output_basename "combined"
-            $log_transform.test  
-            #if $log_transform.test:
-                --log_base $log_transform.log_base
-            #end if
-    ]]></command>
-
-    <inputs>
-        <param name="input_dna" type="data" format="tsv" label="Metagenomic table" 
-            help="(--input_dna)"/>
-        <param name="input_rna" type="data" format="tsv" label="Metatranscriptomic table" 
-            help="(--input_rna)"/>
-
-        <conditional name="log_transform">
-            <param name='test' type='boolean' checked="false" 
-                truevalue='--log_transform' falsevalue='' 
-                label="Report log-transformed relative expression values?" 
-                help="(--log_transform)"/>
-            <when value="--log_transform">
-                <param name="log_base" type="integer" min="0" max="10" value="2" 
-                    label="Base for log transformation" help="(--log_base)"/>
-            </when>
-            <when value=""/>
-        </conditional>        
-    </inputs>
-
-    <outputs>
-        <data format="tsv" name="smoothed_dna" 
-            from_work_dir="combined"
-            label="Smoothed DNA data for ${on_string} (HUMAnN2)" />
-        <data format="tsv" name="smoothed_rna" 
-            from_work_dir="combined"
-            label="Smoothed RNA data for ${on_string} (HUMAnN2)" />
-        <data format="tsv" name="normalized_rna" 
-            from_work_dir="combined"
-            label="Normalized RNA data for ${on_string} (HUMAnN2)" />
-    </outputs>
-
-    <tests>
-    </tests>
-
-    <help><![CDATA[
-        **What it does**
-
-        This tool normalizes combined meta'omic sequencing data. 
-
-        Given a DNA table and a RNA table, it produces smoothed RNA and DNA values as well as relative expression values. "Smoothing" means substituting a small value in place of a zero or missing value. The Witten-Bell smoothing procedure is used here.
-
-        If working with stratified data, smoothing is carried out on the stratified values and then community totals are recomputed.
-
-        The DNA and RNA columns must be 1:1 and in the same order. The units of the table should be count-like (for example, HUMAnN2 gene family abundance files).gene and pathway abundance tables.
-
-        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
-
-    ]]></help>
-
-    <citations>
-    </citations>
-</tool>
\ No newline at end of file
diff -r 0d3d44f13122 -r 7d2be77d5b83 in_development/humann2_split_table.xml
--- a/in_development/humann2_split_table.xml	Mon Feb 22 07:09:45 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<tool id="humann2_split_table" name="Split HUMAnN2 table" version="0.1.0">
-    <description></description>
-
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
-
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-
-    <version_command>
-<![CDATA[
-    \${HUMANN2_DIR}/humann2_split_table --version
-]]>
-    </version_command>
-
-    <command><![CDATA[
-        \${HUMANN2_DIR}/humann2_split_table
-            -i "input_file"
-            -o "output"            
-    ]]></command>
-
-    <inputs>
-        <param name="input_file" type="data" format="tsv,biom" 
-            label="Gene/pathway table to read" help=""/>
-    </inputs>
-
-    <outputs>
-        <outputs>
-            <data format="txt" name="report">
-                <discover_datasets pattern="__designation__" ext="tabular" directory="output" visible="true" />
-            </data>
-        </outputs>
-    </outputs>
-
-    <tests>
-        <test>
-            <param name="input_file" value="humann2_input.fasta"/>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-        **What it does**
-
-        Split HUMAnN2 table is a tool to split a gene/pathway table in table per sample.
-
-        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
-    ]]></help>
-
-    <citations>
-    </citations>
-</tool>
\ No newline at end of file
diff -r 0d3d44f13122 -r 7d2be77d5b83 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Feb 22 07:09:45 2016 -0500
+++ b/tool_dependencies.xml	Thu Mar 31 03:35:17 2016 -0400
@@ -3,13 +3,13 @@
     <package name="bowtie2" version="2.2.5">
         <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="metaphlan2" version="2.0">
-        <repository changeset_revision="d041345c1c7b" name="package_metaphlan_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="metaphlan2" version="2.2.0">
+        <repository changeset_revision="bbac0ef27bb2" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="diamond" version="0.7.10">
         <repository changeset_revision="f3f009bdca19" name="package_diamond_0_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="humann2" version="2.0">
-        <repository changeset_revision="abe443d7f9e7" name="package_humann_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="humann2" version="0.5.0">
+        <repository changeset_revision="831d511bc7a0" name="package_humann2_0_5_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>