Mercurial > repos > rnateam > bctools
changeset 1:ae0f58d3318f draft
Deleted selected files
author | rnateam |
---|---|
date | Thu, 22 Oct 2015 10:22:24 -0400 |
parents | 119fccb59597 |
children | de4ea3aa1090 |
files | convert_bc_to_binary_RY.xml coords2clnt.xml extract_aln_ends.xml extract_bcs.xml macros.xml merge_pcr_duplicates.xml remove_tail.xml rm_spurious_events.xml tool_dependencies.xml |
diffstat | 9 files changed, 0 insertions(+), 386 deletions(-) [+] |
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--- a/convert_bc_to_binary_RY.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -<tool id="convert_bc_to_binary_RY.py" name="convert_bc_to_binary_RY.py" version="0.1.0"> - <description>Convert to binary barcodes.</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command>python convert_bc_to_binary_RY.py --version</version_command> - <command interpreter="python"><![CDATA[ -convert_bc_to_binary_RY.py -#if $positional_1 and $positional_1 is not None: -$positional_1 -#end if -> $default]]></command> - <inputs> - <param label="Fasta file to convert." name="positional_1" type="data" format="fasta"/> - </inputs> - <outputs> - <data hidden="false" name="default" format="fasta"/> - </outputs> - <tests> - <test> - <param name="positional_1" value="result.fa"/> - <output name="default" file="converted_bcs.fa"/> - </test> - </tests> - <help><![CDATA[ -Convert standard nucleotides to IUPAC nucleotide codes used for binary barcodes. - -A and G are converted to nucleotide code R. T, U and C are converted to Y. - -Author: Daniel Maticzka -Copyright: 2015 -License: Apache -Email: maticzkd@informatik.uni-freiburg.de -Status: Testing -]]></help> - <expand macro="citations" /> -</tool>
--- a/coords2clnt.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -<tool id="coords2clnt.py" name="coords2clnt.py" version="1.0"> - <description>Extract crosslinked nucleotide.</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <stdio> - <exit_code level="fatal" range="1:"/> - </stdio> - <version_command>python coords2clnt.py --version</version_command> - <command interpreter="python"><![CDATA[coords2clnt.py -#if $positional_1 and $positional_1 is not None: -$positional_1 -#end if - -> $default]]></command> - <inputs> - <param area="false" label="Alignments in bed format." name="positional_1" type="data" format="bed"/> - </inputs> - <outputs> - <data hidden="false" name="default" format="bed"/> - </outputs> - <tests> - <test> - <param name="positional_1" value="merged_pcr_dupes.bed"/> - <output name="default" file="merged_pcr_dupes_clnts.bed"/> - </test> - </tests> - <help><![CDATA[ -Given coordinates of the aligned reads, calculate positions of the crosslinked nucleotides. -Crosslinked nts are assumed to be one nt upstream of the 5'-end of the read. - -Input: -* bed6 file containing coordinates of aligned reads -* bed6 file containing coordinates of crosslinking events - -Author: Daniel Maticzka -Copyright: 2015 -License: Apache -Email: maticzkd@informatik.uni-freiburg.de -Status: Testing -]]></help> - <expand macro="citations" /> -</tool>
--- a/extract_aln_ends.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -<tool id="extract_aln_ends.py" name="extract_aln_ends.py" version="0.1.0"> - <description>Extract alignment ends from sam file.</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command>python extract_aln_ends.py --version</version_command> - <command interpreter="python"><![CDATA[ -extract_aln_ends.py -#if $positional_1 and $positional_1 is not None: -$positional_1 -#end if - -> $default]]></command> - <inputs> - <param area="false" label="Sam input." name="positional_1" type="data" format="sam"/> - </inputs> - <outputs> - <data format="bed" hidden="false" name="default"/> - </outputs> - <tests> - <test> - <param name="positional_1" value="twomates.sam"/> - <output name="default" file="tworeads_aln_ends.bed"/> - </test> - </tests> - <help><![CDATA[ -Extract alignment ends from sam file. - -The resulting bed file contains the outer coordinates of the alignments. The -bed name field is set to the read id and the score field is set to the edit -distance of the alignment. The crosslinked nucleotide is one nt upstream of the -5'-end of the bed entries. - -This tool only reports results for alignments that are properly aligned in FR -("forward-reverse") direction. - -Input: -* sam file containing alignments (paired-end sequencing) - -Output: -* bed6 file containing outer coordinates (sorted by read id) - -Author: Daniel Maticzka -Copyright: 2015 -License: Apache -Email: maticzkd@informatik.uni-freiburg.de -Status: Development -]]></help> - <expand macro="citations" /> -</tool>
--- a/extract_bcs.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<tool id="extract_bcs.py" name="extract_bcs.py" version="1.0"> - <description>Extract barcodes using pattern.</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command>python extract_bcs.py --version</version_command> - <command interpreter="python"><![CDATA[ -extract_bcs.py -#if $positional_1 and $positional_1 is not None: -$positional_1 -#end if - -#if $positional_2 and $positional_2 is not None: -$positional_2 -#end if - -> $default]]></command> - <inputs> - <param area="false" label="Barcoded sequences." name="positional_1" type="data" format="fastq"/> - <param area="false" label="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept." name="positional_2" type="text"/> - </inputs> - <outputs> - <data hidden="false" name="default" format="fastq" /> - </outputs> - <tests> - <test> - <param name="positional_1" value="reads.fastq"/> - <param name="positional_2" value="XXXNNXXX"/> - <output name="default" file="result.fastq"/> - </test> - </tests> - <help><![CDATA[ -Exract barcodes from a FASTQ file according to a user-specified pattern. - -Author: Daniel Maticzka -Copyright: 2015 -License: Apache -Email: maticzkd@informatik.uni-freiburg.de -Status: Testing -]]></help> - <expand macro="citations" /> -</tool>
--- a/macros.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="0.1.0">bctools</requirement> - </requirements> - </xml> - <xml name="stdio"> - <stdio> - <exit_code level="fatal" range="1:"/> - </stdio> - </xml> - <xml name="citations"> - <citations> - <citation type="doi">10.1016/j.molcel.2013.07.001</citation> - </citations> - </xml> -</macros>
--- a/merge_pcr_duplicates.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -<tool id="merge_pcr_duplicates.py" name="merge_pcr_duplicates.py" version="1.0"> - <description> -</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command>python merge_pcr_duplicates.py --version</version_command> - <command interpreter="python"><![CDATA[merge_pcr_duplicates.py -#if $positional_1 and $positional_1 is not None: -$positional_1 -#end if - -#if $positional_2 and $positional_2 is not None: -$positional_2 -#end if - -> $default]]></command> - <inputs> - <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/> - <param area="false" label="fasta barcode library." name="positional_2" type="data" format="fasta"/> - </inputs> - <outputs> - <data format="bed" hidden="false" name="default"/> - </outputs> - <tests> - <test> - <param name="positional_1" value="pcr_dupes_sorted_2.bed"/> - <param name="positional_2" value="pcr_dupes_randomdict.fa"/> - <output name="default" file="merged_pcr_dupes.bed"/> - </test> - </tests> - <help><![CDATA[ -Merge PCR duplicates according to random barcode library. - -Barcodes containing uncalled base 'N' are removed. - -Input: -* bed6 file containing alignments with fastq read-id in name field -* fasta library with fastq read-id as sequence ids - -Output: -* bed6 file with random barcode in name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name - -Author: Daniel Maticzka -Copyright: 2015 -License: Apache -Email: maticzkd@informatik.uni-freiburg.de -Status: Testing -]]></help> - <expand macro="citations" /> -</tool>
--- a/remove_tail.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -<tool id="remove_tail.py" name="remove_tail.py" version="1.0"> - <description>Remove nts from 3'-end.</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command>python remove_tail.py --version</version_command> - <command interpreter="python"><![CDATA[remove_tail.py -#if $positional_1 and $positional_1 is not None: -$positional_1 -#end if - -#if $positional_2 and $positional_2 is not None: -$positional_2 -#end if - -> $default]]></command> - <inputs> - <param area="false" label="Fastq file." name="positional_1" type="data" format="fastq"/> - <param label="Remove this many nts." name="positional_2" type="integer" value="0"/> - </inputs> - <outputs> - <data format="fastq" hidden="false" name="default"/> - </outputs> - <tests> - <test> - <param name="positional_1" value="readswithtail.fastq"/> - <param name="positional_2" value="7"/> - <output name="default" file="readswithtailremoved.fastq"/> - </test> - </tests> - <help><![CDATA[ -Remove a certain number of nucleotides from the 3'-tails of sequences in fastq format. - -Author: Daniel Maticzka -Copyright: 2015 -License: Apache -Email: maticzkd@informatik.uni-freiburg.de -Status: Testing -]]></help> - <expand macro="citations" /> -</tool>
--- a/rm_spurious_events.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -<tool id="rm_spurious_events.py" name="rm_spurious_events.py" version="1.0"> - <description>Remove spurious events.</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command>python rm_spurious_events.py --version</version_command> - <command interpreter="python"><![CDATA[rm_spurious_events.py -#if $positional_1 and $positional_1 is not None: -$positional_1 -#end if - -#if $threshold and $threshold is not None: ---threshold $threshold -#end if -> $default]]></command> - <inputs> - <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/> - <param help="(--threshold)" label="Threshold for spurious event removal." name="threshold" optional="true" type="float" value="0.1"/> - </inputs> - <outputs> - <data format="bed" hidden="false" name="default"/> - </outputs> - <tests> - <test> - <param name="positional_1" value="merged_pcr_dupes_spurious.bed"/> - <param name="threshold" value="0.5"/> - <output name="default" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/> - </test> - </tests> - <help><![CDATA[ -Remove spurious events originating from errors in random sequence tags. - -This script compares all events sharing the same coordinates. Among each group -of events the maximum number of PCR duplicates is determined. All events that -are supported by less than 10 percent of this maximum count are removed. - -Input: -* bed6 file containing crosslinking events with score field set to number of PCR - duplicates - -Output: -* bed6 file with spurious crosslinking events removed, sorted by fields chrom, - start, stop, strand - -Author: Daniel Maticzka -Copyright: 2015 -License: Apache -Email: maticzkd@informatik.uni-freiburg.de -Status: Testing -]]></help> - <expand macro="citations" /> -</tool>
--- a/tool_dependencies.xml Thu Oct 22 09:52:51 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bctools" version="0.1.0"> - <install version="1.0"> - <actions_group> - <actions> - <action target_filename="bctools-0.1.0-alpha1.tar.gz" type="download_by_url">https://github.com/tzk/bctools/archive/v0.1.0-alpha1.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="b3a791f6e3ba" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="biopython" version="1.65" /> - </repository> - <!-- <repository name="package_python_2_7_pandas_0_16" owner="iuc"> - <package name="pandas" version="0.16" /> - </repository> --> - <repository changeset_revision="045c4645abdf" name="package_pandas_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pandas" version="0.14" /> - </repository> - <!-- <repository name="package_python_2_7_pybedtools_0_6_9" owner="iuc"> - <package name="pybedtools" version="0.6.9" /> - </repository> --> - <repository changeset_revision="372c85bed2ca" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pybedtools" version="0.6.6" /> - </repository> - </action> - <action type="shell_command"> - python setup.py install --install-scripts $INSTALL_DIR - </action> - <action type="set_environment"> - <environment_variable action="set_to" name="BCTOOLS_ROOT_DIR">$INSTALL_DIR</environment_variable> - </action> - </actions> - </actions_group> - </install> - <readme> -bctools - Set of tools for handling barcodes in NGS data. -https://github.com/tzk/bctools - </readme> - </package> -</tool_dependency>