# HG changeset patch
# User mvdbeek
# Date 1498044213 14400
# Node ID 5dcad82862b40991dc3394d809648adc3103cfb6
# Parent  5c32fb616d9559b705dd2e307b9feb13bba274b5
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 3cb122f0ab5dc2ad7bb61d1abdd13865142e25b8-dirty

diff -r 5c32fb616d95 -r 5dcad82862b4 deploy.sh
diff -r 5c32fb616d95 -r 5dcad82862b4 findcluster.xml
--- a/findcluster.xml	Thu May 11 05:33:12 2017 -0400
+++ b/findcluster.xml	Wed Jun 21 07:23:33 2017 -0400
@@ -9,8 +9,17 @@
         ln -f -s $input.metadata.bam_index input.bam.bai &&
         findcluster
         --input_path input.bam
-        #if $reference_fasta:
-            --reference_fasta '$reference_fasta'
+       #if $transposon_reference_fasta:
+            --transposon_reference_fasta '$transposon_reference_fasta'
+        #end if
+        #if $genome_reference_fasta:
+            --genome_reference_fasta '$genome_reference_fasta'
+        #end if
+       #if $transposon_bwa_index:
+            --transposon_bwa_index '$transposon_bwa_index'
+        #end if
+        #if $genome_bwa_index:
+            --genome_bwa_index '$genome_bwa_index'
         #end if
         --output_bam '$output_bam'
         --output_gff '$output_gff'
@@ -20,7 +29,20 @@
     ]]></command>
     <inputs>
         <param name="input" argument="--input_path" type="data" format="bam"/>
-        <param argument="--reference_fasta" label="Reference Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/>
+        <param argument="--transposon_reference_fasta" label="Transposon Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/>
+        <param argument="--genome_reference_fasta" label="Genome Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/>
+        <param argument="--transposon_bwa_index" label="Transposon BWA index" help="Reconstructed contigs at clusters will be blasted against this sequence." type="select" optional="True">
+            <options from_data_table="bwa_mem_indexes">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No indexes are available" />
+            </options>
+        </param>
+        <param argument="--genome_bwa_index" label="Genome BWA index" help="Reconstructed contigs at clusters will be blasted against this sequence." type="select" optional="True">
+            <options from_data_table="bwa_mem_indexes">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No indexes are available" />
+            </options>
+        </param>
     </inputs>
     <outputs>
         <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
@@ -35,7 +57,7 @@
         </test>
         <test>
             <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
-            <param name="reference_fasta" value="reference.fasta" ftype="fasta"/>
+            <param name="transposon_reference_fasta" value="reference.fasta" ftype="fasta"/>
             <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
             <output name="output_gff">
                 <assert_contents>
@@ -64,7 +86,7 @@
       --include_duplicates / --no-include_duplicates
                                       Include reads marked as duplicates when
                                       finding clusters.
-      --reference_fasta TEXT          Blast cluster contigs against this fasta
+      --transposon_reference_fasta TEXT          Blast cluster contigs against this fasta
                                       file
       --blastdb TEXT                  Blast cluster contigs against this blast
                                       database
diff -r 5c32fb616d95 -r 5dcad82862b4 test-data/three_cluster_out.gff
--- a/test-data/three_cluster_out.gff	Thu May 11 05:33:12 2017 -0400
+++ b/test-data/three_cluster_out.gff	Wed Jun 21 07:23:33 2017 -0400
@@ -1,4 +1,3 @@
 ##gff-version 3
-3R	findcluster	TE	13373515	13373524	22	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=1.8828617809e-31,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=11;non_support=0;right_insert=0,GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=11;valid_TSD=False
-3R	findcluster	TE	13374595	13374595	2	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=0.0106846062525,0.329771797916,0.659543595832;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_support=2;non_support=0;right_insert=;right_support=0;valid_TSD=False
-3R	findcluster	TE	13374677	13374677	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=heterozygous;genotype_likelihoods=0.212598425197,0.393700787402;left_insert=;left_support=0;non_support=0;right_insert=;right_support=1;valid_TSD=False
+3R	findcluster	TE	13373515	13373524	22	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=1.8828617809e-31,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_mate_support=8;left_support=11;non_support=0;right_insert=0,GACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_mate_support=6;right_support=11;valid_TSD=False
+3R	findcluster	TE	13374595	13374676	3	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=0.00038864889331,0.199922270221,0.799689080885;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_mate_support=2;left_support=2;non_support=0;right_insert=;right_mate_support=1;right_support=1;valid_TSD=False
diff -r 5c32fb616d95 -r 5dcad82862b4 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Jun 21 07:23:33 2017 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the BWA mapper format for BWA versions 0.6 and higher including BWA MEM and ALN-->
+    <table name="bwa_mem_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bwa_mem_index.loc" />
+    </table>
+</tables>