Mercurial > repos > drosofff > msp_sr_bowtie_parser
changeset 1:ca3845fb0b31 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
| author | drosofff |
|---|---|
| date | Mon, 18 Apr 2016 10:09:08 -0400 |
| parents | b996480cd604 |
| children | |
| files | sRbowtieParser.xml smRtools.py smRtools.pyc tool_dependencies.xml |
| diffstat | 4 files changed, 12 insertions(+), 17 deletions(-) [+] |
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--- a/sRbowtieParser.xml Wed May 27 17:19:15 2015 -0400 +++ b/sRbowtieParser.xml Mon Apr 18 10:09:08 2016 -0400 @@ -1,14 +1,12 @@ -<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1"> +<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6"> <description></description> <requirements> <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="0.7.7">pysam</requirement> <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="0.14">scipy</requirement> </requirements> -<command interpreter="python"> - sRbowtieParser.py +<command> + python $__tool_directory__/sRbowtieParser.py #if $refGenomeSource.genomeSource == "history": --IndexSource $refGenomeSource.ownFile --ExtractDirective fastaSource @@ -29,7 +27,7 @@ #end for --alignmentLabel #for $i in $refGenomeSource.input_list - "$i.name" + "$i.element_identifier" #end for </command> @@ -40,13 +38,13 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> + <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"> <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> - <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> + <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/> </when> </conditional> <!-- refGenomeSource --> <param name="polarity" type="select" label="how to count sense and antisense reads">
--- a/smRtools.py Wed May 27 17:19:15 2015 -0400 +++ b/smRtools.py Mon Apr 18 10:09:08 2016 -0400 @@ -4,7 +4,8 @@ import sys, subprocess from collections import defaultdict from numpy import mean, median, std -from scipy import stats +##Disable scipy import temporarily, as no working scipy on toolshed. +##from scipy import stats def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"): '''This function will return a dictionary containing fasta identifiers as keys and the @@ -273,6 +274,8 @@ def correlation_mapper (self, reference, window_size): '''to map correlation with a sliding window 26-2-2013''' + from scipy import stats + if window_size > self.size: return [] F=open(reference, "r")
--- a/tool_dependencies.xml Wed May 27 17:19:15 2015 -0400 +++ b/tool_dependencies.xml Mon Apr 18 10:09:08 2016 -0400 @@ -3,16 +3,10 @@ <package name="bowtie" version="0.12.7"> <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> <package name="pysam" version="0.7.7"> - <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.9"> - <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="scipy" version="0.14"> - <repository changeset_revision="d470054f3a5d" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c8f7a7d73466" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>