Mercurial > repos > bebatut > humann2
changeset 8:0d3d44f13122 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 313952cc4a20e8fb82380bfbf5ede26217197719
| author | bebatut |
|---|---|
| date | Mon, 22 Feb 2016 07:09:45 -0500 |
| parents | d084f63fbf30 |
| children | 7d2be77d5b83 |
| files | humann2.xml humann2_join_tables.xml humann2_reduce_table.xml humann2_regroup_table.xml humann2_rename_table.xml humann2_renorm_table.xml in_development/humann2_merge_abundance_tables.xml in_development/humann2_regroup_table.xml in_development/humann2_rna_dna_norm.xml in_development/humann2_split_table.xml tool_dependencies.xml |
| diffstat | 11 files changed, 108 insertions(+), 123 deletions(-) [+] |
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--- a/humann2.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/humann2.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,16 +14,12 @@ <version_command> <![CDATA[ - humann2 --version + \${HUMANN2_DIR}/humann2 --version ]]> </version_command> <command><![CDATA[ - (which diamond || exit 200) - - && - - humann2 + \${HUMANN2_DIR}/humann2 -i "$input_file" #if $taxonomic_profile.taxonomic_profile_test:
--- a/humann2_join_tables.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/humann2_join_tables.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,7 +14,7 @@ <version_command> <![CDATA[ - humann2_join_tables --version + \${HUMANN2_DIR}/humann2_join_tables --version ]]> </version_command> @@ -27,7 +27,7 @@ #end for && - humann2_join_tables + \${HUMANN2_DIR}/humann2_join_tables -i "tmp_dir" -o $joined_table ]]></command>
--- a/humann2_reduce_table.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/humann2_reduce_table.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,12 +14,12 @@ <version_command> <![CDATA[ - humann2_reduce_table --version + \${HUMANN2_DIR}/humann2_reduce_table --version ]]> </version_command> <command><![CDATA[ - humann2_reduce_table + \${HUMANN2_DIR}/humann2_reduce_table -i $input_table -o $output_table --function $function
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/humann2_regroup_table.xml Mon Feb 22 07:09:45 2016 -0500 @@ -0,0 +1,91 @@ +<tool id="humann2_regroup_table" name="Regroup HUMAnN2 table features" 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_regroup_table --version +]]> + </version_command> + + <command><![CDATA[ + \${HUMANN2_DIR}/humann2_regroup_table + -i $input_table + -o $output_table + --function $function + + #if $built_in.test: + --groups $built_in.groups + #else: + --custom $built_in.file + $built_in.reversed + #end if + ]]></command> + + <inputs> + <param name="input_table" type="data" format="tsv" label="Gene/pathway + table" help=""/> + + <param name="function" type="select" label="How to combine grouped features?" help="(--function)"> + <option value="sum" selected="true">Sum</option> + <option value="mean">Mean</option> + </param> + + <conditional name="built_in"> + <param name='test' type='boolean' checked="false" truevalue='true' + falsevalue='false' label="Use built-in grouping options?" + help=""/> + <when value="true"> + <param name="groups" type="select" label="Grouping options" help="(--groups)"> + <option value="uniref50_ec" selected="true">Collapses UniRef50 gene families into top level enzyme commission (EC) categories (associations inferred from UniProt)</option> + <option value="uniref50_go">Collapses UniRef50 gene families into a subset of non-redundant, high-level Gene Ontology (GO) categories (associations inferred from UniProt and a HUMAnN2-specific parsing of the GO hierarchy)</option> + <option value="uniref50_ko">Collapses UniRef50 gene fammilies into KEGG Orthogroups (KOs) (associations inferred from UniProt)</option> + <option value="uniref50_rxn">Collapses UniRef50 gene families into metacyc reactions (use of reaction abundances to compute the abundance and coverage of broader metabolic pathways)</option> + </param> + </when> + <when value="false"> + <param name="file" type="data" format="tsv" label="Custom groups file" help="(--custom)"/> + <param name='reversed' type='boolean' checked="false" truevalue='--reversed' + falsevalue='' label="Is the groups file reversed?" + help="Mapping from features to groups. (--reversed)"/> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tsv" name="output_table" label="Regrouped table for + ${on_string} (HUMAnN2)" /> + </outputs> + + <tests> + <test> + <param name="input_table" value="humann2_fasta_pathabundance.tsv"/> + <param name="function" value="sum"/> + <param name="test" value="true"/> + <param name="groups" value="uniref50_ec"/> + <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/> + </test> + </tests> + + <help><![CDATA[ + **What it does** + + Regroup HUMAnN2 table features is a tool for egrouping table features. Given a table of feature values and a mapping of groups to component features, produce a new table with group values in place of feature values. + + 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_rename_table.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/humann2_rename_table.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,12 +14,12 @@ <version_command> <![CDATA[ - humann2_rename_table --version + \${HUMANN2_DIR}/humann2_rename_table --version ]]> </version_command> <command><![CDATA[ - humann2_rename_table + \${HUMANN2_DIR}/humann2_rename_table -i $input_table -o $output_table
--- a/humann2_renorm_table.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/humann2_renorm_table.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,12 +14,12 @@ <version_command> <![CDATA[ - humann2_renorm_table --version + \${HUMANN2_DIR}/humann2_renorm_table --version ]]> </version_command> <command><![CDATA[ - humann2_renorm_table + \${HUMANN2_DIR}/humann2_renorm_table -i $input_table -o $output_table --norm $norm
--- a/in_development/humann2_merge_abundance_tables.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/in_development/humann2_merge_abundance_tables.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,12 +14,12 @@ <version_command> <![CDATA[ - humann2_merge_abundance_tables --version + \${HUMANN2_DIR}/humann2_merge_abundance_tables --version ]]> </version_command> <command><![CDATA[ - humann2_merge_abundance_tables + \${HUMANN2_DIR}/humann2_merge_abundance_tables --input-genes $input_gene --input-pathways $input_pathway --gene-mapping $gene_mapping
--- a/in_development/humann2_regroup_table.xml Fri Dec 18 09:04:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,91 +0,0 @@ -<tool id="humann2_regroup_table" name="Regroup HUMAnN2 table features" 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_regroup_table --version -]]> - </version_command> - - <command><![CDATA[ - humann2_regroup_table - -i $input_table - -o $output_table - --function $function - - #if $built_in.test: - --groups $built_in.groups - #else: - --custom $built_in.file - $built_in.reversed - #end if - ]]></command> - - <inputs> - <param name="input_table" type="data" format="tsv" label="Gene/pathway - table" help=""/> - - <param name="function" type="select" label="How to combine grouped features?" help="(--function)"> - <option value="sum" selected="true">Sum</option> - <option value="mean">Mean</option> - </param> - - <conditional name="built_in"> - <param name='test' type='boolean' checked="false" truevalue='true' - falsevalue='false' label="Use built-in grouping options?" - help=""/> - <when value="true"> - <param name="groups" type="select" label="Grouping options" help="(--groups)"> - <option value="uniref50_ec" selected="true">Collapses UniRef50 gene families into top level enzyme commission (EC) categories (associations inferred from UniProt)</option> - <option value="uniref50_go">Collapses UniRef50 gene families into a subset of non-redundant, high-level Gene Ontology (GO) categories (associations inferred from UniProt and a HUMAnN2-specific parsing of the GO hierarchy)</option> - <option value="uniref50_ko">Collapses UniRef50 gene fammilies into KEGG Orthogroups (KOs) (associations inferred from UniProt)</option> - <option value="uniref50_rxn">Collapses UniRef50 gene families into metacyc reactions (use of reaction abundances to compute the abundance and coverage of broader metabolic pathways)</option> - </param> - </when> - <when value="false"> - <param name="file" type="data" format="tsv" label="Custom groups file" help="(--custom)"/> - <param name='reversed' type='boolean' checked="false" truevalue='--reversed' - falsevalue='' label="Is the groups file reversed?" - help="Mapping from features to groups. (--reversed)"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tsv" name="output_table" label="Regrouped table for - ${on_string} (HUMAnN2)" /> - </outputs> - - <tests> - <test> - <param name="input_table" value="humann2_fasta_pathabundance.tsv"/> - <param name="function" value="sum"/> - <param name="test" value="true"/> - <param name="groups" value="uniref50_ec"/> - <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/> - </test> - </tests> - - <help><![CDATA[ - **What it does** - - Regroup HUMAnN2 table features is a tool for egrouping table features. Given a table of feature values and a mapping of groups to component features, produce a new table with group values in place of feature values. - - 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 Fri Dec 18 09:04:07 2015 -0500 +++ b/in_development/humann2_rna_dna_norm.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,12 +14,12 @@ <version_command> <![CDATA[ - humann2_rna_dna_norm --version + \${HUMANN2_DIR}/humann2_rna_dna_norm --version ]]> </version_command> <command><![CDATA[ - humann2_rna_dna_norm + \${HUMANN2_DIR}/humann2_rna_dna_norm --input_dna $input_dna --input_rna $input_rna --output_basename "combined"
--- a/in_development/humann2_split_table.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/in_development/humann2_split_table.xml Mon Feb 22 07:09:45 2016 -0500 @@ -14,12 +14,12 @@ <version_command> <![CDATA[ - humann2_split_table --version + \${HUMANN2_DIR}/humann2_split_table --version ]]> </version_command> <command><![CDATA[ - humann2_split_table + \${HUMANN2_DIR}/humann2_split_table -i "input_file" -o "output" ]]></command>
--- a/tool_dependencies.xml Fri Dec 18 09:04:07 2015 -0500 +++ b/tool_dependencies.xml Mon Feb 22 07:09:45 2016 -0500 @@ -10,17 +10,6 @@ <repository changeset_revision="f3f009bdca19" name="package_diamond_0_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="humann2" version="2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://bitbucket.org/biobakery/humann2/downloads/humann2_v0.5.0.tar.gz</action> - <action type="shell_command">python setup.py install --bypass-dependencies-install</action> - <action type="make_directory">$INSTALL_DIR/databases</action> - <action type="set_environment"> - <environment_variable action="set_to" name="HUMANN2_DIR">$INSTALL_DIR/</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme /> + <repository changeset_revision="abe443d7f9e7" name="package_humann_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>