Mercurial > repos > artbio > repenrich
changeset 4:d1f7ab78f7b5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
| author | artbio |
|---|---|
| date | Sun, 18 Nov 2018 12:53:01 -0500 |
| parents | 1c9810ba0638 |
| children | 02a8941da83b |
| files | RepEnrich.py repenrich.xml test-data/Samp.fastq.gz test-data/Samp_L.fastq.gz test-data/Samp_R.fastq.gz |
| diffstat | 5 files changed, 40 insertions(+), 8 deletions(-) [+] |
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--- a/RepEnrich.py Fri Sep 22 03:19:23 2017 -0400 +++ b/RepEnrich.py Sun Nov 18 12:53:01 2018 -0500 @@ -1,10 +1,7 @@ -#!/usr/bin/env python - import argparse import csv import os import shlex - import shutil import subprocess import sys
--- a/repenrich.xml Fri Sep 22 03:19:23 2017 -0400 +++ b/repenrich.xml Sun Nov 18 12:53:01 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="1.4.3"> +<tool id="repenrich" name="RepEnrich" version="1.5.0"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -13,11 +13,25 @@ #import re #set input_base = 'Sample' #set baseReference = 'Genome' + + ## uncompress fastq.gz or fastqsanger.gz if needed + #if $seq_method.seq_method_list == "single-read": + #if $input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): + gunzip < '$input_fastq' > '${input_base}.fastq' && + #else: + ln -f -s '$input_fastq' '${input_base}.fastq' && + #end if + #else: + #if $input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): + gunzip < '$input_fastq' > '${input_base}.fastq' && + gunzip < '$input2_fastq' > '${input_base}_2.fastq' && + #else: + ln -f -s '$input_fastq' '${input_base}.fastq' && + ln -f -s '$input2_fastq' '${input_base}_2.fastq' && + #end if + #end if + ln -f -s '$genome' '${baseReference}.fa' && - ln -f -s '$input_fastq' '${input_base}.fastq' && - #if $seq_method.seq_method_list == "paired-end": - ln -f -s '$input2_fastq' '${input_base}_2.fastq' && - #end if bowtie-build '$genome' ${baseReference} && python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && #if $seq_method.seq_method_list == "single-read": @@ -95,6 +109,27 @@ <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/> <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/> </test> + <test> + <param name="seq_method_list" value="single-read"/> + <param name="input_fastq" value="Samp.fastq.gz" ftype="fastq.gz"/> + <param name="genome" value="chrM.fa" ftype="fasta"/> + <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> + <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/> + <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/> + <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> + <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/> + </test> + <test> + <param name="seq_method_list" value="paired-end"/> + <param name="input_fastq" value="Samp_L.fastq.gz" ftype="fastq.gz"/> + <param name="input2_fastq" value="Samp_R.fastq.gz" ftype="fastq.gz"/> + <param name="genome" value="chrM.fa" ftype="fasta"/> + <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> + <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/> + <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/> + <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/> + <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/> + </test> </tests> <help>