Mercurial > repos > iuc > hivclustering
diff hivclustering.xml @ 0:ef842bb94d1f draft default tip
planemo upload for repository https://github.com/veg/hivclustering/ commit 7d666f963da2c5e3b17c313526cc6169f3242c3c
| author | iuc |
|---|---|
| date | Thu, 14 Jun 2018 07:04:38 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hivclustering.xml Thu Jun 14 07:04:38 2018 -0400 @@ -0,0 +1,123 @@ +<?xml version="1.0"?> +<tool id="hivclustering" name="Make inferences" version="@VERSION@.0"> + <description>on HIV-1 transmission networks using HIVClustering</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + hivnetworkcsv --input '$input' $cluster $multiple_edges $singletons $centralities + --threshold $threshold --exclude $exclude --triangles $triangles --format $format + #if $contamination.contaminants != 'ignore': + --contaminants $contamination.contaminants + --contaminant-file '$contamination.contaminant_file' + #end if + #if $edges.edge_filtering != 'ignore': + --edge-filtering $edges.edge_filtering + --sequences '$sequences' + #end if + #if $uds: + --uds '$uds' + #end if + #if $edi: + --edi '$edi' + #end if + #if $old_edi: + --old_edi '$old_edi' + #end if + #if $resistance: + --resistance '$resistance' + #end if + #if $attributes: + --attributes '$attributes' + #end if + #if $filter: + --filter '$filter' + #end if + --json > hivcluster.json + ]]> + </command> + <inputs> + <param argument="--input" type="data" format="csv" multiple="True" label="Input file with inferred links"/> + <conditional name="contamination"> + <param argument="--contaminants" type="select" label="How to treat contamination"> + <option value="ignore" selected="True">Do nothing</option> + <option value="report">Report</option> + <option value="remove">Remove</option> + </param> + <when value="ignore"/> + <when value="report"> + <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/> + </when> + <when value="remove"> + <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/> + </when> + </conditional> + <conditional name="edges"> + <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges"> + <option value="ignore" selected="True">Do not mark</option> + <option value="report">For display</option> + <option value="remove">For removal</option> + </param> + <when value="ignore"/> + <when value="report"> + <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/> + </when> + <when value="remove"> + <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/> + </when> + </conditional> + <param argument="--uds" type="data" format="csv" optional="True" label="Input file with UDS data"/> + <param argument="--edi" type="data" format="json" optional="True" label="Input JSON with clinical information"/> + <param argument="--old_edi" type="data" format="csv" optional="True" label="Legacy EDI dates in CSV format"/> + <param argument="--resistance" type="data" format="csv" optional="True" label="Resistance annotation in JSON format"/> + <param argument="--attributes" type="data" format="csv" optional="True" label="Input CSV with node attributes"/> + <param argument="--filter" type="data" format="text" optional="True" label="File with IDs to cluster, one per line"/> + <param argument="--format" type="select" label="Sequence ID format"> + <option value="AEH">AEH</option> + <option value="LANL">LANL</option> + <option value="plain">plain</option> + </param> + <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence"/> + <param name="multiple_edges" argument="--multiple-edges" type="boolean" truevalue="--multiple-edges" falsevalue="" label="Permit multiple edges to link the same pair of nodes in the network"/> + <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output"/> + <param argument="--centralities" type="boolean" truevalue="--centralities" falsevalue="" label="Output a CSV file with node centralities"/> + <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold"/> + <param argument="--exclude" type="integer" value="1959" label="Only consider sequences isolated after this year"/> + <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/> + </inputs> + <outputs> + <data name="graph" from_work_dir="hivcluster.json" format="hivtrace"/> + </outputs> + <tests> + <test> + <param name="input" value="hivclustering-in1.csv" ftype="csv"/> + <param name="format" value="plain"/> + <param name="threshold" value="0.8"/> + <param name="json" value="True"/> + <output name="graph" ftype="hivtrace"> + <assert_contents> + <has_text text="Cluster sizes"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="hivclustering-in2.csv" ftype="csv"/> + <param name="format" value="plain"/> + <param name="threshold" value="0.8"/> + <param name="json" value="True"/> + <output name="graph" ftype="hivtrace"> + <assert_contents> + <has_text text="Cluster sizes"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +HIVClustering +------------- + +A python library that makes inferences on HIV-1 transmission networks. + ]]></help> + <expand macro="citations"/> +</tool>