Mercurial > repos > mvdbeek > bam_readtagger
changeset 32:5dcad82862b4 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 3cb122f0ab5dc2ad7bb61d1abdd13865142e25b8-dirty
author | mvdbeek |
---|---|
date | Wed, 21 Jun 2017 07:23:33 -0400 |
parents | 5c32fb616d95 |
children | a01f2a172eeb |
files | deploy.sh findcluster.xml test-data/three_cluster_out.gff tool_data_table_conf.xml.sample |
diffstat | 3 files changed, 37 insertions(+), 8 deletions(-) [+] |
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--- 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
--- 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
--- /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>