# HG changeset patch
# User mvdbeek
# Date 1521112858 14400
# Node ID 432bb619c079a35f3a174aa716a08ca07d912b01
# Parent  f6311a04a6c968d143015624b600e9ca1e97c8fa
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty

diff -r f6311a04a6c9 -r 432bb619c079 filter_insertions.xml
--- a/filter_insertions.xml	Thu Mar 15 05:13:22 2018 -0400
+++ b/filter_insertions.xml	Thu Mar 15 07:20:58 2018 -0400
@@ -5,10 +5,13 @@
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
+        ln -fs $putative_insertions putative_insertions.gff &&
+        ln -fs $all_insertions all_insertions.gff &&
+        ln -fs $all_controls all_controls_path.gff &&
         confirm_insertions
-        --putative_insertions_path '$putative_insertions'
-        --all_treatments_path '$all_insertions'
-        --all_controls_path '$all_controls'
+        --putative_insertions_path putative_insertions.gff
+        --all_treatments_path all_insertions.gff
+        --all_controls_path all_controls_path.gff
         --output_path '$output'
         $output_discard
     ]]></command>
@@ -16,7 +19,7 @@
         <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
         <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
         <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/>
-        <param name="output_discard" label="Output discarded records? Thye will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
+        <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
     </inputs>
     <outputs>
         <data name="output" format="gff3"/>
diff -r f6311a04a6c9 -r 432bb619c079 test-data/confirmed_insertions.gff
--- a/test-data/confirmed_insertions.gff	Thu Mar 15 05:13:22 2018 -0400
+++ b/test-data/confirmed_insertions.gff	Thu Mar 15 07:20:58 2018 -0400
@@ -1,2 +1,3 @@
+TEST	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
 X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
 X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True;FAIL=clip_seq_in_control
diff -r f6311a04a6c9 -r 432bb619c079 test-data/putative_insertions.gff
--- a/test-data/putative_insertions.gff	Thu Mar 15 05:13:22 2018 -0400
+++ b/test-data/putative_insertions.gff	Thu Mar 15 07:20:58 2018 -0400
@@ -1,2 +1,3 @@
+TEST	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True
 X	findcluster	transposable_element_rover	10766937	10766942	24	+	.	ID=R37_49;genotype=heterozygous;genotype_likelihoods=6.86863481923e-26,0.999999994797,5.2033283093e-09;insert_reference_name=transposable_element_rover;left_inserts=0,GGGGTGCATATATAGCGCACATATGTACATATTTGTACATATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCA,1,CAACAATGTATTATCCTACCGACTGCGCCACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATCAACGCCTTTAAAGAAGTTTCAGAATCAACACGAGGTATTTTTTTAGTTTGGA;left_mate_count=4;max_mapq=60;nref=12;right_inserts=0,GGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATACATATGCATATGCAGTCCGAATCAAAATCGAAAACAAGAACTGCACTTTTCGCTGCGATTGGGGCACCTTCAGC,1,GTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCCGTTCTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTAT,2,CACATATACTGATTAGACATTCCCGTTTATCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTT;right_mate_count=14;total_left_count=6;total_right_count=18;valid_TSD=True
 X	findcluster	jockey2	16727068	16727111	6	+	.	ID=R37_27;genotype=heterozygous;genotype_likelihoods=8.55882087985e-05,0.999914411654,1.37666001367e-10;insert_reference_name=jockey2;left_inserts=;left_mate_count=0;max_mapq=25;nref=9;right_inserts=0,GATATGGACTTAATTGGAAATTAATTAATGCAATAATCCAATTAAGAATTTAATATTTAAAAAGGTGGACTGAATACTTAATACAAGAAGGATAATAGTACGCTAGTCAATTAAATAAAATAATTTCTTTAATAAAATTAAAGGAC;right_mate_count=2;total_left_count=3;total_right_count=4;valid_TSD=True