# HG changeset patch
# User wolma
# Date 1469087749 14400
# Node ID 5db0545b9004a4d15a6c97502ad8e8d4a73d2a4e
# Parent 24154c5807186714b06fa7e67b17a5cc560ffeb5
update to v0.1.7.3
diff -r 24154c580718 -r 5db0545b9004 annotate_variants.xml
--- a/annotate_variants.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/annotate_variants.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-
+Predict the effects of SNPs and indels on known genes in the reference genome using SnpEfftoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD annotate
@@ -50,65 +50,65 @@
-
-
+
+
-
+
-
-
+
+
-
+
-
-
+
+
-
-
+
+
-
-
+
+
-
+
## default settings for SnpEff
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
@@ -116,15 +116,15 @@
-
+
-
+
-
+
(annotool['name']=="snpeff" and annotool['ori_output'])
-
+
(annotool['name']=="snpeff" and annotool['stats'])
@@ -166,5 +166,4 @@
.. _tell us about the problem: mailto:mimodd@googlegroups.com
-
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 bamsort.xml
--- a/bamsort.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/bamsort.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-
+Sort a BAM file by coordinates (or names) of the mapped readstoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
@@ -11,28 +11,28 @@
-
+
-
+
-
+
-
+
-
+
-
+
-
+
@@ -49,5 +49,4 @@
The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.
-
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 cloudmap.xml
--- a/cloudmap.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/cloudmap.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,7 +1,6 @@
-
+Map causative mutations by multi-variant linkage analysis.
-
- python3 -m MiModD version -q
+ python3 -m MiModD version -q
python3 -m MiModD map ${opt.mode} "${opt.source.ifile}"
#if $str($opt.source.sample):
@@ -62,16 +61,16 @@
-
+
-
+
-
-
+
+
@@ -81,9 +80,9 @@
-
+
-
+
@@ -91,8 +90,8 @@
-
-
+
+
@@ -100,12 +99,12 @@
-
-
+
+
-
+
@@ -120,7 +119,7 @@
-
+
@@ -135,39 +134,39 @@
-
+
-
+
-
+
-
-
-
+
+
+
-
+
-
+
-
+
@@ -175,27 +174,27 @@
-
+
-
+
-
+
-
+
-
+
@@ -203,26 +202,26 @@
-
+
-
+
-
-
-
-
+
+
+
+
-
+
-
+
@@ -234,11 +233,11 @@
-
-
+
+
(opt['source']['tabfile'])
-
+
(opt['source']['plotopts']['plots'])
@@ -337,4 +336,4 @@
.. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
.. _mapping-by-sequencing analysis workflows in MiModD: http://mimodd.readthedocs.org/en/latest/cloudmap.html
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 convert.xml
--- a/convert.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/convert.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,13 +1,13 @@
-
+between different sequence data formatstoolshed_macros.xml
-
+ python3 -m MiModD version -q
#if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz":
- echo "Your input data is now getting processed by MiModD. The output will be split into several files based on the read groups found in the input.\nThis history item will remain in the busy state until the job is finished.\nAfter the job is showing as finished, Galaxy will start adding the results files to your history one by one.\n\nThis may take a while to complete! \n\nYou should refresh your history to see if new files have arrived.\n\nThis message is for your information only and can be deleted from the history once the job has finished." > $output_split_on_read_groups;
+ echo "Your input data is now getting processed by MiModD. The output will be split into several files based on the read groups found in the input.\nThis history item will remain in the busy state until the job is finished.\nAfter the job is showing as finished, Galaxy will start adding the results files to your history one by one.\n\nThis may take a while to complete! \n\nYou should refresh your history to see if new files have arrived.\n\nThis message is for your information only and can be deleted from the history once the job has finished." > $output_split_on_read_groups;
mkdir converted_data;
#end if
@@ -36,7 +36,7 @@
-
+
@@ -45,95 +45,95 @@
-
+
-
-
+
+
-
-
+
+
-
+
-
-
-
+
+
+
-
-
+
+
-
+
-
-
+
+
-
-
+
+
-
+
-
-
-
+
+
+
-
-
+
+
-
+
-
-
+
+
-
-
+
+
-
+
-
-
+
+
-
-
+
+
-
+
-
+
(not mode['split_on_rgs'] and mode['oformat'] not in ("fastq", "gz"))
-
+
(mode['split_on_rgs'] or mode['oformat'] in ("fastq", "gz"))
-
+
@@ -167,5 +167,4 @@
.. _MiModD user guide: http://mimodd.readthedocs.org/en/latest
-
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 covstats.xml
--- a/covstats.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/covstats.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,19 +1,19 @@
-
+Calculate coverage statistics for a BCF file as generated by the Variant Calling tooltoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD covstats "$ifile" --ofile "$output_vcf"
-
+
-
+
@@ -28,4 +28,4 @@
The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites.
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 deletion_predictor.xml
--- a/deletion_predictor.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/deletion_predictor.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-
+Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizestoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD delcall
@@ -15,18 +15,18 @@
-
-
+
+
-
-
-
-
-
+
+
+
+
+
-
+
@@ -62,4 +62,4 @@
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 fileinfo.xml
--- a/fileinfo.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/fileinfo.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,26 +1,26 @@
-
+for supported data formats.toolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD info "$ifile" -o "$outputfile" --verbose --oformat $oformat
-
-
+
+
-
+
-
+
@@ -35,4 +35,4 @@
It autodetects and works with most file formats produced by MiModD, i.e., **SAM / BAM, vcf / bcf and fasta**, and produces a standardized report for all of them.
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 reheader.xml
--- a/reheader.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/reheader.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,6 +1,6 @@
-
+From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file
-
+ python3 -m MiModD version -q
#if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
@@ -103,29 +103,29 @@
toolshed_macros.xml
-
+
-
-
-
-
+
+
+
+
-
-
+
+
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
@@ -134,10 +134,10 @@
-
+
-
+
@@ -151,37 +151,37 @@
-
+
-
-
+
+
-
-
+
+
-
-
-
+
+
+
-
-
-
+
+
+
-
+
@@ -199,5 +199,4 @@
The template information used to modify or replace the input file metadata is provided through forms or, in the case of read-group information, can be taken from an existing SAM file as can be generated, for example, with the *NGS Run Annotation* tool.
-
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 sam_header.xml
--- a/sam_header.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/sam_header.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-
+Create a SAM format header from run metadata for sample annotation.toolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD header
@@ -38,73 +38,73 @@
-
+
-
+
-
+
-
+
-
+
-
+
-
-
+
+
-
+
-
+
-
+
-
-
-
+
+
+
-
+
-
+
@@ -125,5 +125,4 @@
While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, we **recommend** you to first convert all input files to and archive all datasets in SAM/BAM format with appropriate header information prior to any downstream analysis. Although a bit more time-consuming, this practice protects against information loss and ensures that the input datasets will remain useful for others in the future.
-
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 snap_caller.xml
--- a/snap_caller.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/snap_caller.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-
+Map sequence reads to a reference genome using SNAPtoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD snap-batch -s
@@ -50,73 +50,73 @@
## mandatory arguments (and mode-conditionals)
-
+
-
+
-
+
-
+
-
-
+
+
-
-
+
+
-
-
+
+
-
-
+
+
-
+
-
-
+
+
-
-
+
+
-
-
-
+
+
+
-
-
-
+
+
+
-
+
@@ -124,7 +124,7 @@
## optional arguments
-
+
@@ -132,58 +132,58 @@
## default settings
-
-
-
-
-
-
-
+
+
+
+
+
+
+
-
-
-
+
+
+
-
-
-
-
+
+
+
+
## change settings
-
-
+
+
## paired-end specific options
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
-
-
+
+
-
+
-
+
@@ -192,9 +192,9 @@
-
+
-
+
@@ -238,5 +238,4 @@
.. _tool documentation: http://mimodd.readthedocs.org/en/latest/tool_doc.html#snap
-
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 snp_caller_caller.xml
--- a/snp_caller_caller.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/snp_caller_caller.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-
+From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage informationtoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD varcall
@@ -21,17 +21,17 @@
-
-
-
+
+
+
-
-
-
+
+
+
-
+
@@ -63,4 +63,4 @@
It exposes just a single configuration parameter of these tools - the *maximum per-BAM depth*. Through this parameter, the maximum number of reads considered for variant calling at any site can be controlled. Its default value of 250 is taken from *samtools mpileup* and usually suitable. Consider, however, that this gives the maximum read number per input file, so if you have a large number of samples in one input file, it could become necessary to increase the value to get sufficient reads considered per sample.
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 snpeff_genomes.xml
--- a/snpeff_genomes.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/snpeff_genomes.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,15 +1,15 @@
-
+Checks the local SnpEff installation to compile a list of currently installed genomestoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD snpeff-genomes -o "$outputfile"
-
+
.. class:: infomark
@@ -21,4 +21,4 @@
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 tool_dependencies.xml
--- a/tool_dependencies.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/tool_dependencies.xml Thu Jul 21 03:55:49 2016 -0400
@@ -13,7 +13,7 @@
-
+
@@ -62,9 +62,9 @@
$TMP_WORK_DIR
- http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz
- tar -xzf MiModD-0.1.7.2.tar.gz
- MiModD-0.1.7.2
+ http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.3/MiModD-0.1.7.3.tar.gz
+ tar -xzf MiModD-0.1.7.3.tar.gz
+ MiModD-0.1.7.3
diff -r 24154c580718 -r 5db0545b9004 toolshed_macros.xml
--- a/toolshed_macros.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/toolshed_macros.xml Thu Jul 21 03:55:49 2016 -0400
@@ -2,13 +2,13 @@
python3
- mimodd
+ mimoddpython3
- mimodd
+ mimoddRreadline
diff -r 24154c580718 -r 5db0545b9004 varextract.xml
--- a/varextract.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/varextract.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,11 +1,11 @@
-
+from a BCF filetoolshed_macros.xml
-
+ python3 -m MiModD version -q
-
+
python3 -m MiModD varextract "$ifile"
#if $len($sitesinfo)
-p
@@ -19,14 +19,14 @@
-
-
-
+
+
+
-
+
-
+
@@ -98,4 +98,4 @@
-
+
\ No newline at end of file
diff -r 24154c580718 -r 5db0545b9004 vcf_filter.xml
--- a/vcf_filter.xml Sun Jun 12 07:39:46 2016 -0400
+++ b/vcf_filter.xml Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-
+Extracts lines from a vcf variant file based on field-specific filterstoolshed_macros.xml
-
+ python3 -m MiModD version -q
python3 -m MiModD vcf-filter
@@ -52,29 +52,29 @@
-
-
-
-
-
-
-
+
+
+
+
+
+
+
-
-
-
-
+
+
+
+
-
+
-
+
-
+
@@ -105,21 +105,21 @@
*Simple genotype pattern*
-genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant
+genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant
*Complex genotype pattern*
-genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype
+genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype
*Multiple sample-specific filters*
Filter 1: genotype pattern: 0/0, Filter 2: genotype pattern 1/1:
-==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant
+==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant
*Combining sample-specific filter criteria*
genotype pattern: 1/1, depth of coverage: 3, genotype quality: 9
-==> keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9
+==> keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9
**and** at least three reads from the sample cover the variant site
**TIP:**
@@ -130,4 +130,4 @@
-
+
\ No newline at end of file