# HG changeset patch
# User rnateam
# Date 1445523744 14400
# Node ID ae0f58d3318faf4f553156ed21d954fbb3ecef92
# Parent  119fccb5959729bc176618aaaedf0cb391993cdc
Deleted selected files

diff -r 119fccb59597 -r ae0f58d3318f convert_bc_to_binary_RY.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f coords2clnt.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f extract_aln_ends.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f extract_bcs.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f macros.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f merge_pcr_duplicates.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f remove_tail.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f rm_spurious_events.xml
--- 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>
diff -r 119fccb59597 -r ae0f58d3318f tool_dependencies.xml
--- 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>