# HG changeset patch
# User bebatut
# Date 1464272459 14400
# Node ID 3d6f37e7e3a84fc6c0adce445c385a825d99cae4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
diff -r 000000000000 -r 3d6f37e7e3a8 humann2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2.xml Thu May 26 10:20:59 2016 -0400
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+ to profile presence/absence and abundance of microbial pathways and gene families
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+ humann2_macros.xml
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+ output_format == "tsv"
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+ output_format == "biom"
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+ output_format == "tsv"
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+ output_format == "biom"
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+ output_format == "tsv"
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+ output_format == "biom"
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+ `_.
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+This tool corresponds to the main tool in HUMAnN2 pipeline.
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+**Inputs**
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+The input is a single file corresponding either to filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format), alignment file (sam, bam or blastm8 format) or gene table file (tsv or biom format).
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+A file with a taxonomic profile (obtained with MetaPhlan2) can also be provided to avoid first step of taxonomic profiling needed to select pangenomes in protein database.
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+HUMAnN2 uses multiple databases. Locally cached nucleotide or protein databases have to be downloaded database before using them (using the dedicated tool). Custom databases can also be used after upload. Nucleotide database have to be provided as a dataset.
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+**Outputs**
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+HUMAnN creates three output files:
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+ - A file with gene families and their abundance
+ - A file with pathways and their abundance
+ - A file with pathways and their coverage
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+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_download_databases.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_download_databases.xml Thu May 26 10:20:59 2016 -0400
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+ HUMAnN2 databases
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+ humann2_macros.xml
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+ $log
+ ]]>
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+ `_.
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+Download HUMAnN2 databases is a tool to download needed nucleotide or protein databases. This tool must be run before using HUMAnN2.
+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_join_tables.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_join_tables.xml Thu May 26 10:20:59 2016 -0400
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+ HUMAnN2 generated tables
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+ humann2_macros.xml
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+ `_.
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+Join HUMAnN2 tables is a tool to join gene or pathway tables of multiple samples into a single table.
+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_macros.xml Thu May 26 10:20:59 2016 -0400
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+ bowtie2
+ metaphlan2
+ diamond
+ humann2
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+ 10.1371/journal.pcbi.1002358
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_merge_abundance_tables.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_merge_abundance_tables.xml Thu May 26 10:20:59 2016 -0400
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+ HUMAnN2 generated gene and pathway abundance tables
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+ humann2_macros.xml
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+ `_.
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+The currest tool merge a table containing gene family abundances with a table containing pathway abundances, given a gene to pathway mapping (default or custom one).
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+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_reduce_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_reduce_table.xml Thu May 26 10:20:59 2016 -0400
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+ a HUMAnN2 generated table
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+ humann2_macros.xml
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+ `_.
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+Reduce HUMAnN2 table is a tool to reduce the table given a function (max, sum, mean or min).
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+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 `_.
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+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_regroup_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_regroup_table.xml Thu May 26 10:20:59 2016 -0400
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+ a HUMAnN2 generated table by features
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+ humann2_macros.xml
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+ `_.
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+Regroup HUMAnN2 table features is a tool for regrouping table features (abundances or coverage) given a table of feature values and a mapping of groups to component features. It produces a new table with group values in place of feature values.
+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_rename_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_rename_table.xml Thu May 26 10:20:59 2016 -0400
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+ features of a HUMAnN2 generated table
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+ humann2_macros.xml
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+ `_.
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+Rename HUMAnN2 table features is a tool for renaming table features given a custom mapping. The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new valu
+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_renorm_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_renorm_table.xml Thu May 26 10:20:59 2016 -0400
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+ a HUMAnN2 generated table
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+ `_.
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+Renorm HUMAnN2 table is a tool to renormalize a table, either in copies per million or in relative abundance. Each level of a stratified table will be normalized using the desired scheme.
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+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 humann2_split_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_split_table.xml Thu May 26 10:20:59 2016 -0400
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+ a HUMAnN2 generated table
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+ humann2_macros.xml
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+ `_.
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+Split HUMAnN2 table is a tool to split a table with multiple columns. This file can have been generated with the join table tool.
+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 3d6f37e7e3a8 test-data/cpm_renormalized_pathway_abundance.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cpm_renormalized_pathway_abundance.tsv Thu May 26 10:20:59 2016 -0400
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+# Pathway humann2_Abundance
+UNMAPPED 5956.49
+UNINTEGRATED 983482
+PWY-3841: folate transformations II 3222.17
+HOMOSER-METSYN-PWY: L-methionine biosynthesis I 2969.34
+HSERMETANA-PWY: L-methionine biosynthesis III 2555.95
+VALSYN-PWY: L-valine biosynthesis 1813.8