Mercurial > repos > rdvelazquez > hivclustering
changeset 2:9dc36a1975e8 draft
planemo upload for repository https://github.com/veg/hivclustering/ commit b'a6d09759f16c40d4607d30f4bb28772e74c07021\n'-dirty
| author | rdvelazquez |
|---|---|
| date | Thu, 19 Apr 2018 14:39:39 -0400 |
| parents | d975f8166fc8 |
| children | 8a6f3d2a2d23 |
| files | hivclustering.xml macros.xml test-data/hivclustering-in1.csv test-data/hivclustering-in2.csv test-data/hivclustering-out1.json test-data/hivclustering-out2.json |
| diffstat | 6 files changed, 914 insertions(+), 890 deletions(-) [+] |
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--- a/hivclustering.xml Mon Mar 05 10:57:10 2018 -0500 +++ b/hivclustering.xml Thu Apr 19 14:39:39 2018 -0400 @@ -1,111 +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="hmmer3" multiple="True" label="Input multi-sequence alignment" /> - </when> - <when value="remove"> - <param argument="--sequences" type="data" format="hmmer3" 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="json" /> - </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="output" ftype="json" file="hivclustering-out1.json" /> - </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="output" ftype="json" file="hivclustering-out2.json" /> - </test> - </tests> - <help>A Python 3 library that makes inferences on HIV-1 transmission networks.</help> -</tool> - +<?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>
--- a/macros.xml Mon Mar 05 10:57:10 2018 -0500 +++ b/macros.xml Thu Apr 19 14:39:39 2018 -0400 @@ -1,9 +1,21 @@ -<?xml version="1.0"?> -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="@VERSION@">python-hivclustering</requirement> - </requirements> - </xml> - <token name="@VERSION@">1.3.0</token> -</macros> \ No newline at end of file +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">python-hivclustering</requirement> + </requirements> + </xml> + <token name="@VERSION@">1.3.1</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{spond, + author = "Sergei Kosakovsky Pond", + title = "HyPhy: Hypothesis Testing using Phylogenies", + year = "2000", + note = "http://hyphy.org/", + url = "http://hyphy.org/"} + </citation> + </citations> + </xml> +</macros>
--- a/test-data/hivclustering-in1.csv Mon Mar 05 10:57:10 2018 -0500 +++ b/test-data/hivclustering-in1.csv Thu Apr 19 14:39:39 2018 -0400 @@ -1,8 +1,8 @@ -ID1,ID2,Distance -B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994 -B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156 -D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974 -B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328 -B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218 -D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246 -B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566 +ID1,ID2,Distance +B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994 +B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156 +D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974 +B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328 +B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218 +D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246 +B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566
--- a/test-data/hivclustering-in2.csv Mon Mar 05 10:57:10 2018 -0500 +++ b/test-data/hivclustering-in2.csv Thu Apr 19 14:39:39 2018 -0400 @@ -1,29 +1,29 @@ -ID1,ID2,Distance -B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994 -B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856 -B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797 -B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156 -B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328 -B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097 -B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218 -B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044 -B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908 -B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203 -B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566 -B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011 -B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759 -B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019 -B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206 -B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066 -B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054 -D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246 -B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586 -B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146 -D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974 -D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948 -B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619 -B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213 -D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626 -B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988 -D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033 -D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088 +ID1,ID2,Distance +B_US_86_JRFL_ACC_U63632,B_US_90_WEAU160_ACC_U21135,0.0408994 +B_US_90_WEAU160_ACC_U21135,D_CD_83_ELI_ACC_K03454_7,0.0771856 +B_US_86_JRFL_ACC_U63632,D_CD_83_ELI_ACC_K03454_7,0.0771797 +B_FR_83_HXB2_ACC_K03455_5,B_US_83_RF_ACC_M17451,0.045156 +B_US_83_RF_ACC_M17451,B_US_86_JRFL_ACC_U63632,0.048328 +B_US_90_WEAU160_ACC_U21135,D_CD_83_NDK_ACC_M27323,0.0609097 +B_FR_83_HXB2_ACC_K03455_5,B_US_86_JRFL_ACC_U63632,0.0296218 +B_US_86_JRFL_ACC_U63632,D_CD_83_NDK_ACC_M27323,0.0609044 +B_US_83_RF_ACC_M17451,B_US_90_WEAU160_ACC_U21135,0.0515908 +B_US_90_WEAU160_ACC_U21135,D_CD_84_84ZR085_ACC_U88822,0.0740203 +B_FR_83_HXB2_ACC_K03455_5,B_US_90_WEAU160_ACC_U21135,0.0327566 +B_US_86_JRFL_ACC_U63632,D_CD_84_84ZR085_ACC_U88822,0.0705011 +B_US_83_RF_ACC_M17451,D_CD_83_ELI_ACC_K03454_7,0.0810759 +B_US_90_WEAU160_ACC_U21135,D_UG_94_94UG114_ACC_U88824,0.0890019 +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_ELI_ACC_K03454_7,0.0669206 +B_US_83_RF_ACC_M17451,D_CD_83_NDK_ACC_M27323,0.0661066 +B_US_86_JRFL_ACC_U63632,D_UG_94_94UG114_ACC_U88824,0.0882054 +D_CD_83_ELI_ACC_K03454_7,D_CD_83_NDK_ACC_M27323,0.0287246 +B_FR_83_HXB2_ACC_K03455_5,D_CD_83_NDK_ACC_M27323,0.0592586 +B_US_83_RF_ACC_M17451,D_CD_84_84ZR085_ACC_U88822,0.0769146 +D_CD_83_NDK_ACC_M27323,D_CD_84_84ZR085_ACC_U88822,0.0491974 +D_CD_83_ELI_ACC_K03454_7,D_CD_84_84ZR085_ACC_U88822,0.055948 +B_FR_83_HXB2_ACC_K03455_5,D_CD_84_84ZR085_ACC_U88822,0.0663619 +B_US_83_RF_ACC_M17451,D_UG_94_94UG114_ACC_U88824,0.0955213 +D_CD_83_NDK_ACC_M27323,D_UG_94_94UG114_ACC_U88824,0.0726626 +B_FR_83_HXB2_ACC_K03455_5,D_UG_94_94UG114_ACC_U88824,0.0847988 +D_CD_83_ELI_ACC_K03454_7,D_UG_94_94UG114_ACC_U88824,0.0742033 +D_CD_84_84ZR085_ACC_U88822,D_UG_94_94UG114_ACC_U88824,0.0805088
--- a/test-data/hivclustering-out1.json Mon Mar 05 10:57:10 2018 -0500 +++ b/test-data/hivclustering-out1.json Thu Apr 19 14:39:39 2018 -0400 @@ -1,206 +1,206 @@ -{ - "Cluster sizes": [ - 4, - 3 - ], - "Degrees": { - "Distribution": [ - 2, - 3, - 2 - ], - "Model": "Waring", - "fitted": [ - 0.5000721527871422, - 0.24996196530120798, - 0.12496295268484243 - ], - "rho": 3287.8967604237114, - "rho CI": [ - 698.4419473417928, - 10000.0 - ] - }, - "Directed Edges": { - "Count": 0, - "Reasons for unresolved directions": { - "Missing dates": 7 - } - }, - "Edges": [ - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.045156, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "B_US_83_RF_ACC_M17451" - ], - "source": 2, - "support": 0.0, - "target": 3 - }, - { - "attributes": [ - "BULK" - ], - "directed": false, - "length": 0.0296218, - "removed": false, - "sequences": [ - "B_FR_83_HXB2_ACC_K03455_5", - "B_US_86_JRFL_ACC_U63632" - ], - "source": 2, - "support": 0.0, - 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