# HG changeset patch
# User charles-bernard
# Date 1513866566 18000
# Node ID b26aec436ab55f8536925ffe748de9cb6f824aa2
# Parent 7df7bee710adc34d5b00fe4966b62d0c4c471475
Uploaded
diff -r 7df7bee710ad -r b26aec436ab5 ALFA/.shed.yml
--- a/ALFA/.shed.yml Sun Dec 18 09:50:39 2016 -0500
+++ b/ALFA/.shed.yml Thu Dec 21 09:29:26 2017 -0500
@@ -7,8 +7,8 @@
long_description: |
ALFA provides a global overview of features distribution composing New Generation Sequencing dataset(s).
Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.
- https://github.com/biocompibens/ALFA.git
+ https://github.com/biocompibens/ALFA
name: alfa
owner: charles_bernard
-remote_repository_url: https://github.com/charles-bernard/Galaxy_tools/tree/master/ALFA
-type: unrestricted
\ No newline at end of file
+remote_repository_url: https://github.com/biocompibens/ALFA/tree/master/Galaxy_toolshed_repositories/ALFA
+type: unrestricted
diff -r 7df7bee710ad -r b26aec436ab5 ALFA/ALFA.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ALFA/ALFA.xml Thu Dec 21 09:29:26 2017 -0500
@@ -0,0 +1,329 @@
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+ - Plot the distribution of genomic features in your aligned reads
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+ bedtools
+ samtools
+ matplotlib
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+ outputFiles['plot'] is True and outputOptions['plotFormat'] == 'pdf'
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+ outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'
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+ outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'
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+ outputFiles['plot'] is True and outputOptions['plotFormat'] == 'svg'
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+ outputFiles['plot'] is True and outputOptions['plotFormat'] == 'svg'
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+ outputFiles['countFile'] is True
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+ outputFiles['index'] is True
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+ outputFiles['index'] is True
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+ @MISC{
+ author="Benoît Noël and Mathieu Bahin"
+ title="ALFA: Annotation Landscape For Aligned reads"
+ crossref="https://github.com/biocompibens/ALFA"
+ institution="Institut de Biologie de l'Ecole Normale Supérieure de Paris"
+ }
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diff -r 7df7bee710ad -r b26aec436ab5 ALFA/ALFA_wrapper.py
--- a/ALFA/ALFA_wrapper.py Sun Dec 18 09:50:39 2016 -0500
+++ b/ALFA/ALFA_wrapper.py Thu Dec 21 09:29:26 2017 -0500
@@ -54,6 +54,10 @@
n = len(reads_list)
if n%2 != 0:
exit_and_explain('Problem with pairing reads filename and reads label')
+ if format == 'bam':
+ input2_args = '--bam'
+ elif format == 'begraph':
+ input2_args = '--bedgraph'
input2_args='-i'
k = 0
reads_filenames = [''] * (n/2)
@@ -66,8 +70,6 @@
reads_labels[k] = 'sample_%s' % str(k)
input2_args='%s "%s" "%s"' % (input2_args, reads_filenames[k], reads_labels[k])
k += 1
- if format == 'bedgraph':
- input2_args = input2_args + ' --bedgraph'
return input2_args, reads_filenames, reads_labels
def redirect_errors(alfa_out, alfa_err):
diff -r 7df7bee710ad -r b26aec436ab5 ALFA/alfa_wrapper.xml
--- a/ALFA/alfa_wrapper.xml Sun Dec 18 09:50:39 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,329 +0,0 @@
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- - Compute and display distribution of reads by genomic categories
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- bedtools
- samtools
- matplotlib
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- outputFiles['plot'] is True and outputOptions['plotFormat'] == 'pdf'
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- outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'
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- outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'
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- outputFiles['plot'] is True and outputOptions['plotFormat'] == 'svg'
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- outputFiles['plot'] is True and outputOptions['plotFormat'] == 'svg'
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- outputFiles['countFile'] is True
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- outputFiles['index'] is True
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- @MISC{
- author="Benoît Noël and Mathieu Bahin"
- title="ALFA: Annotation Landscape For Aligned reads"
- crossref="https://github.com/biocompibens/ALFA"
- institution="Institut de Biologie de l'Ecole Normale Supérieure de Paris"
- }
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diff -r 7df7bee710ad -r b26aec436ab5 ALFA/tool_dependencies.xml
--- a/ALFA/tool_dependencies.xml Sun Dec 18 09:50:39 2016 -0500
+++ b/ALFA/tool_dependencies.xml Thu Dec 21 09:29:26 2017 -0500
@@ -1,11 +1,12 @@
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