Mercurial > repos > drosofff > msp_sr_signature
changeset 1:6218b518cd16 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
| author | drosofff |
|---|---|
| date | Wed, 07 Jun 2017 17:53:44 -0400 |
| parents | a2f293717ce3 |
| children | 229645380cb9 |
| files | signature.py signature.xml smRtools.py tool_dependencies.xml |
| diffstat | 4 files changed, 24 insertions(+), 80 deletions(-) [+] |
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--- a/signature.py Wed Oct 21 11:35:25 2015 -0400 +++ b/signature.py Wed Jun 07 17:53:44 2017 -0400 @@ -2,15 +2,13 @@ # script for computing overlap signatures from a bowtie output # Christophe Antoniewski <drosofff@gmail.com> # Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target> -# <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedure option> <12: graph (global or lattice)> -# <13: R code> +# <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedure option> <12: graph (global or lattice)> +# <13: R code> # version 2.0.0 -import sys import subprocess import argparse -from smRtools import * -from collections import defaultdict # test whether it is required +from smRtools import HandleSmRNAwindows def Parser():
--- a/signature.xml Wed Oct 21 11:35:25 2015 -0400 +++ b/signature.xml Wed Jun 07 17:53:44 2017 -0400 @@ -1,16 +1,16 @@ -<tool id="signature" name="Small RNA Signatures" version="2.0.5"> +<tool id="signature" name="Small RNA Signatures" version="2.1.0"> <description /> <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="0.7.7">pysam</requirement> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="2.14">biocbasics</requirement> - <requirement type="package" version="1.9">numpy</requirement> + <requirement type="package" version="1.1.2">bowtie</requirement> + <requirement type="package" version="1.11.2=py27_0">numpy</requirement> + <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> + <!-- <requirement type="package" version="3.1.2">R</requirement> --> + <requirement type="package" version="0.20_33=r3.2.2_0a">r-lattice</requirement> </requirements> - <command interpreter="python"> - signature.py - --input $refGenomeSource.input - --inputFormat $refGenomeSource.input.ext + <command><![CDATA[ + python '$__tool_directory__'/signature.py + --input '$refGenomeSource.input' + --inputFormat '$refGenomeSource.input.ext' --minquery $minquery --maxquery $maxquery --mintarget $mintarget @@ -19,15 +19,15 @@ --maxscope $maxscope --outputOverlapDataframe $output #if $refGenomeSource.genomeSource == "history": - --referenceGenome $refGenomeSource.ownFile + --referenceGenome '$refGenomeSource.ownFile' #else: #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] - --referenceGenome $reference + --referenceGenome '$reference' --extract_index #end if --graph $graph_type - --rcode $sigplotter - </command> + --rcode '$sigplotter' + ]]></command> <inputs> <conditional name="refGenomeSource"> <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
--- a/smRtools.py Wed Oct 21 11:35:25 2015 -0400 +++ b/smRtools.py Wed Jun 07 17:53:44 2017 -0400 @@ -142,26 +142,6 @@ self.alignedReads += 1 F.close() return self.instanceDict -# elif self.alignmentFileFormat == "sam": -# F = open (self.alignmentFile, "r") -# dict = {"0":"+", "16":"-"} -# for line in F: -# if line[0]=='@': -# continue -# fields = line.split() -# if fields[2] == "*": continue -# polarity = dict[fields[1]] -# gene = fields[2] -# offset = int(fields[3]) -# size = len (fields[9]) -# if self.size_inf: -# if (size>=self.size_inf and size<= self.size_sup): -# self.instanceDict[gene].addread (polarity, offset, size) -# self.alignedReads += 1 -# else: -# self.instanceDict[gene].addread (polarity, offset, size) -# self.alignedReads += 1 -# F.close() elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam": import pysam samfile = pysam.Samfile(self.alignmentFile) @@ -184,22 +164,6 @@ self.alignedReads += 1 return self.instanceDict -# def size_histogram (self): -# size_dict={} -# size_dict['F']= defaultdict (int) -# size_dict['R']= defaultdict (int) -# size_dict['both'] = defaultdict (int) -# for item in self.instanceDict: -# buffer_dict_F = self.instanceDict[item].size_histogram()['F'] -# buffer_dict_R = self.instanceDict[item].size_histogram()['R'] -# for size in buffer_dict_F: -# size_dict['F'][size] += buffer_dict_F[size] -# for size in buffer_dict_R: -# size_dict['R'][size] -= buffer_dict_R[size] -# allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) ) -# for size in allSizeKeys: -# size_dict['both'][size] = size_dict['F'][size] + size_dict['R'][size] -# return size_dict def size_histogram (self): # in HandleSmRNAwindows '''refactored on 7-9-2014 to debug size_histogram tool''' size_dict={} @@ -361,24 +325,7 @@ for offset in range (min(dicsize.keys()), max(dicsize.keys())+1): dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values return dicsize - -# def size_histogram(self): -# norm=self.norm -# hist_dict={} -# hist_dict['F']={} -# hist_dict['R']={} -# for offset in self.readDict: -# for size in self.readDict[offset]: -# if offset < 0: -# hist_dict['R'][size] = hist_dict['R'].get(size, 0) - 1*norm -# else: -# hist_dict['F'][size] = hist_dict['F'].get(size, 0) + 1*norm -# ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate ! -# if not (hist_dict['F']) and (not hist_dict['R']): -# hist_dict['F'][21] = 0 -# hist_dict['R'][21] = 0 -# ## -# return hist_dict + def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow '''refactored on 7-9-2014 to debug size_histogram tool''' @@ -480,7 +427,6 @@ return ". | %s" % (freqDic["Trev"] / reverse_sum * 100) else: return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100) - def readplot (self): norm=self.norm
--- a/tool_dependencies.xml Wed Oct 21 11:35:25 2015 -0400 +++ b/tool_dependencies.xml Wed Jun 07 17:53:44 2017 -0400 @@ -1,16 +1,16 @@ <?xml version="1.0"?> <tool_dependency> - <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 name="bowtie" version="1.1.2"> + <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="pysam" version="0.7.7"> - <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="pysam" version="0.8.3"> + <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.9"> - <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="3.1.2"> - <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="biocbasics" version="2.14"> <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />