Mercurial > repos > portiahollyoak > temp
changeset 10:3200a0299230 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d
| author | portiahollyoak |
|---|---|
| date | Wed, 27 Apr 2016 11:44:13 -0400 |
| parents | 20a6e46295d6 |
| children | e19d9742c99b |
| files | temp.xml tool_dependencies.xml |
| diffstat | 2 files changed, 28 insertions(+), 4 deletions(-) [+] |
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--- a/temp.xml Tue Apr 26 06:36:46 2016 -0400 +++ b/temp.xml Wed Apr 27 11:44:13 2016 -0400 @@ -1,11 +1,17 @@ -<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1"> +<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2"> <description></description> <requirements> - <requirement type="package" version="0.1.19">samtools</requirement> + <!-- The following are classical toolshed packages and should be removed + once conda is deemed stable--> + <requirement type="package" version="1.6.922">bioperl</requirement> + <requirement type="package" version="0.7.12">bwa</requirement> + <requirement type="package" version="2.24">bedtools</requirement> + <!-- end of toolshed package definitions --> <requirement type="package" version="1.6.924">perl-bioperl</requirement> <requirement type="package" version="0.7.13">bwa</requirement> <requirement type="package" version="2.25.0">bedtools</requirement> <requirement type="package" version="324">ucsc-twobittofa</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -14,7 +20,7 @@ ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && ln -f -s "$alignment" alignment.sorted.bam && - bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && ls -l && + bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && mv alignment.insertion.bp.bed $insertion_bed && mv alignment.insertion.refined.bp $insertion_bed_refined && @@ -67,4 +73,4 @@ ]]> </help> -</tool> \ No newline at end of file +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 27 11:44:13 2016 -0400 @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bioperl" version="1.6.922"> + <repository changeset_revision="52a377d1c8de" name="package_bioperl_1_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="perl" version="5.18.1"> + <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bedtools" version="2.24"> + <repository changeset_revision="39b86c1e267d" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bwa" version="0.7.12"> + <repository changeset_revision="6af9b24ddeee" name="package_bwa_0_7_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>