Mercurial > repos > mvdbeek > bam_readtagger

changeset 4:7625c594bc37 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
author mvdbeek
date Thu, 02 Mar 2017 09:02:27 -0500
parents cb9036583afe
children a3c2c0f6abc9
files add_matesequence.xml allow_dovetailing.xml bam_readtagger.xml findcluster.xml test-data/extended_and_annotated_roi.bam test-data/tagged_dm6.bam test-data/three_cluster_out.bam test-data/three_cluster_out.gff test.sh
diffstat 9 files changed, 59 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/add_matesequence.xml	Tue Feb 21 04:39:31 2017 -0500
+++ b/add_matesequence.xml	Thu Mar 02 09:02:27 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.2.0">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.0">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.2.0">readtagger</requirement>
+        <requirement type="package" version="0.3.0">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
--- a/allow_dovetailing.xml	Tue Feb 21 04:39:31 2017 -0500
+++ b/allow_dovetailing.xml	Thu Mar 02 09:02:27 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.2.0">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.0">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.2.0">readtagger</requirement>
+        <requirement type="package" version="0.3.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
--- a/bam_readtagger.xml	Tue Feb 21 04:39:31 2017 -0500
+++ b/bam_readtagger.xml	Thu Mar 02 09:02:27 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.2.0">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.0">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.2.0">readtagger</requirement>
+        <requirement type="package" version="0.3.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findcluster.xml	Thu Mar 02 09:02:27 2017 -0500
@@ -0,0 +1,47 @@
+<tool id="findcluster" name="Find clusters of reads" version="0.3.0">
+    <description>in bam files</description>
+    <requirements>
+        <requirement type="package" version="0.3.0">readtagger</requirement>
+    </requirements>
+    <version_command>findcluster --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        findcluster
+        --input_path '$input'
+        --output_bam '$output_bam'
+        --output_gff '$output_gff'
+        --sample_name '$input.element_identifier'
+    ]]></command>
+    <inputs>
+        <param name="input" argument="--input_path" type="data" format="bam"/>
+    </inputs>
+    <outputs>
+        <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
+        <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
+            <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
+            <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. code-block::
+
+    Find clusters of reads that support a TE insertion.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --input_path INPUT_PATH
+                            Find cluster in this BAM file. (default: None)
+      --output_bam OUTPUT_BAM
+                            Write out BAM file with cluster information to this
+                            path. Reads will have an additional "CD" tag to
+                            indicate the cluster number (default: None)
+      --output_gff OUTPUT_GFF
+                            Write out GFF file with cluster information to this
+                            path. (default: None)
+      --version             show program's version number and exit
+
+]]></help>
+</tool>
Binary file test-data/extended_and_annotated_roi.bam has changed
Binary file test-data/tagged_dm6.bam has changed
Binary file test-data/three_cluster_out.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/three_cluster_out.gff	Thu Mar 02 09:02:27 2017 -0500
@@ -0,0 +1,6 @@
+##gff-version 3
+3R	findcluster	TE	13373515	13373524	39	+	.	ID=extended_and_annotated_roi.bam_0;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=26;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False
+##gff-version 3
+3R	findcluster	TE	13374595	13374595	2	+	.	ID=extended_and_annotated_roi.bam_1;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_support=2;right_insert=;right_support=0;valid_TSD=False
+##gff-version 3
+3R	findcluster	TE	13374677	13374677	1	+	.	ID=extended_and_annotated_roi.bam_2;left_insert=;left_support=0;right_insert=;right_support=1;valid_TSD=False
--- a/test.sh	Tue Feb 21 04:39:31 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-if grep -v 'python tag_reads.py' bam_tag_reads.xml
-then
-    sed -i.bak 's/tag_reads -t/python \$__tool_directory__\/tag_reads.py -t/g' bam_tag_reads.xml
-fi
-cp ../tag_reads/tag_reads.py .
-planemo test --conda_prefix ~/miniconda3