Mercurial > repos > ulfschaefer > phemost
changeset 11:2e0e0e196386 draft
Deleted selected files
| author | ulfschaefer |
|---|---|
| date | Fri, 08 Jul 2016 10:34:44 -0400 |
| parents | 4adc881442c3 |
| children | a984d5b727d8 |
| files | tool_data_table_conf.xml.sample MOST.sh MOST.xml tool_dependencies.xml |
| diffstat | 4 files changed, 0 insertions(+), 118 deletions(-) [+] |
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--- a/ tool_data_table_conf.xml.sample Fri Jul 08 10:31:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<?xml version="1.0"?> -<tables> - <table name="mlst_data" comment_char="#"> - <columns>value, dbkey, name, time_stamp, file_path</columns> - <file path="tool-data/mlst_data.loc" /> - </table> -</tables>
--- a/MOST.sh Fri Jul 08 10:31:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -#!/bin/bash - -echo $@ - -FWDFILE=$1 -shift -REVFILE=$1 -shift -OUTXML=$1 -shift -OUTCSV=$1 -shift -ORGANISM=$1 - -OUTFOLDER=$(mktemp -d --tmpdir tmpMOST_XXXXXXXXXXXXXXXXXXXX) -rm -rf $OUTFOLDER # MOST insists on creating the folder itself - -CMD="MOST.py -1 $FWDFILE -2 $REVFILE -o $OUTFOLDER -st $ORGANISM" - -echo $CMD -eval $CMD - -STEM=$(basename $FWDFILE) -STEM="${STEM%.*}" - -mv $OUTFOLDER"/"$STEM"_MLST_result.csv" $OUTCSV -mv "$OUTFOLDER/$STEM.results.xml" $OUTXML - -rm -rf $OUTFOLDER
--- a/MOST.xml Fri Jul 08 10:31:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -<tool id="most" name="MOST"> - <description>Determine MLST from sequencing reads</description> - - <requirements> - <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="3.2.3">lxml</requirement> - <requirement type="package" version="3.11">pyyaml</requirement> - <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="1.66">biopython</requirement> - <requirement type="package" version="2.1.0">bowtie2</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> - <requirement type="package" version="5.0.0">emboss</requirement> - <requirement type="package" version="2.2.27">blast_plus</requirement> - <requirement type="package" version="1.0">phemost</requirement> - </requirements> - - <command interpreter="bash"> - MOST.sh - $fwd_file - $rev_file - $out1 - $out2 - "${organism.fields.file_path}" - </command> - - <inputs> - <param name="fwd_file" type="data" format="fastq" label="Read dataset for direction 1" help="Select fastq R1 here."/> - <param name="rev_file" type="data" format="fastq" label="Read dataset for direction 2" help="Select fastq R2 here."/> - <param name="organism" type="select" label="Select an organism"> - <options from_data_table="mlst_data"> - <column name="value" index="0"/> - <column name="dbkey" index="1"/> - <column name="name" index="2"/> - <column name="time_stamp" index="3"/> - <column name="file_path" index="4"/> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </inputs> - - <outputs> - <data name="out1" format="xml" label="${fwd_file.name}: MLST result XML"/> - <data name="out2" format="csv" label="${fwd_file.name}: MLST result CSV"/> - </outputs> - - <help> - https://github.com/phe-bioinformatics/MOST - </help> -</tool>
--- a/tool_dependencies.xml Fri Jul 08 10:31:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="python" version="2.7.10"> - <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="lxml" version="3.2.3"> - <repository changeset_revision="a735146d1bcf" name="package_python_2_7_lxml_3_2_3" owner="ulfschaefer" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="pyyaml" version="3.11"> - <repository changeset_revision="2fc38063906e" name="package_python_2_7_pyyaml_3_11" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="numpy" version="1.9"> - <repository changeset_revision="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="biopython" version="1.66"> - <repository changeset_revision="81243480cf23" name="package_python_2_7_biopython_1_66" owner="ulfschaefer" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="bowtie2" version="2.1.0"> - <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="f499719dad6e" name="package_samtools_0_1_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="emboss" version="5.0.0"> - <repository changeset_revision="423c17dafd88" name="package_emboss_5_0_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="blast+" version="2.2.27"> - <repository changeset_revision="44fa0f193887" name="package_blast_plus_2_2_27" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> - <package name="phemost" version="1.0"> - <repository changeset_revision="4ca8862e8ed6" name="package_phemost_1_0" owner="ulfschaefer" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - </package> -</tool_dependency>