Mercurial > repos > bebatut > humann2
changeset 18:2caada2d49bc draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'adf695285ea7366d6c5d48e416c4e00d83b9e733\n'-dirty
author | bebatut |
---|---|
date | Thu, 02 Mar 2017 09:25:07 -0500 |
parents | 156f73f155e3 |
children | 8192fbe69c0e |
files | humann2.xml repository_dependencies.xml |
diffstat | 2 files changed, 3 insertions(+), 12 deletions(-) [+] |
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--- a/humann2.xml Thu Mar 02 03:36:58 2017 -0500 +++ b/humann2.xml Thu Mar 02 09:25:07 2017 -0500 @@ -1,10 +1,8 @@ <tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.0"> <description>to profile presence/absence and abundance of microbial pathways and gene families</description> - <macros> <import>humann2_macros.xml</import> </macros> - <expand macro="requirements"> <requirement type="package" version="2.3.0">bowtie2</requirement> <requirement type="package" version="2.6.0">metaphlan2</requirement> @@ -13,10 +11,8 @@ <requirement type="package" version="2.7.10">python</requirement> </expand> <expand macro="stdio"/> - <version_command><![CDATA[ humann2 --version ]]> </version_command> - <command><![CDATA[ #if $nucleotide_db.nucleotide_db_selector == "history" mkdir nucleotide_db @@ -114,7 +110,6 @@ $remove_column_description_output --pathways '$pathways' ]]></command> - <inputs> <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom" label="Input sequence file" help=""/> <param name='bypass_prescreen' argument='--bypass-prescreen' type='boolean' checked="false" truevalue='--bypass-prescreen' falsevalue='' label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/> @@ -127,7 +122,7 @@ <option value="history">From history (as collection)</option> </param> <when value="cached"> - <param name="nucleotide_database" type="select" label="Nucleotide database" help=""> + <param name="nucleotide_database" type="select" label="Nucleotide database"> <options from_data_table="humann2_nucleotide_database"/> </param> </when> @@ -142,7 +137,7 @@ <option value="history">From history</option> </param> <when value="cached"> - <param name="protein_database" type="select" label="Protein database" help=""> + <param name="protein_database" type="select" label="Protein database"> <options from_data_table="humann2_protein_database"/> </param> </when> @@ -206,7 +201,6 @@ <option value="unipathway">UniPathway</option> </param> </inputs> - <outputs> <data format="tsv" name="gene_families_tsv" from_work_dir="output/humann2_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" > <filter>output_format == "tsv"</filter> @@ -227,7 +221,6 @@ <filter>output_format == "biom"</filter> </data> </outputs> - <tests> <test> <param name="input" value="input_sequences.fasta"/> @@ -336,7 +329,6 @@ </output> </test> </tests> - <help><![CDATA[ **What it does** @@ -381,6 +373,5 @@ - A file with pathways and their coverage ]]></help> - <expand macro="citations"/> </tool>
--- a/repository_dependencies.xml Thu Mar 02 03:36:58 2017 -0500 +++ b/repository_dependencies.xml Thu Mar 02 09:25:07 2017 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories description="This requires the HUMAnN2 data manager definition to install all required databases."> <repository changeset_revision="8602983cb86f" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - <repository changeset_revision="71114ccf1026" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a0eed08a6b61" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>