Mercurial > repos > bebatut > humann2
changeset 9:7d2be77d5b83 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
| author | bebatut |
|---|---|
| date | Thu, 31 Mar 2016 03:35:17 -0400 |
| parents | 0d3d44f13122 |
| children | a749062bc435 |
| files | README.md humann2.xml humann2_join_tables.xml humann2_macros.xml humann2_merge_abundance_tables.xml humann2_reduce_table.xml humann2_regroup_table.xml humann2_rename_table.xml humann2_renorm_table.xml humann2_rna_dna_norm.xml humann2_split_table.xml in_development/humann2_merge_abundance_tables.xml in_development/humann2_rna_dna_norm.xml in_development/humann2_split_table.xml tool_dependencies.xml |
| diffstat | 15 files changed, 278 insertions(+), 362 deletions(-) [+] |
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--- 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
--- 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>
--- 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>
--- /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
--- /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
--- 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
--- 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
--- 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
--- 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
--- /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
--- /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
--- 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
--- 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
--- 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
--- 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>