Mercurial > repos > portiahollyoak > temp
changeset 15:65ae84fc6689 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 7e0a7a19ee51f12bdcdfe84f3de67530a8990de9
| author | portiahollyoak |
|---|---|
| date | Mon, 23 May 2016 10:37:52 -0400 |
| parents | bc39ae53be03 |
| children | c613f8c96e6d |
| files | temp.xml test-data/median_insert_size |
| diffstat | 2 files changed, 23 insertions(+), 9 deletions(-) [+] |
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--- a/temp.xml Mon May 23 06:53:10 2016 -0400 +++ b/temp.xml Mon May 23 10:37:52 2016 -0400 @@ -1,4 +1,4 @@ -<tool id ="run_TEMP" name="TEMP" version=" 0.1.5"> +<tool id ="run_TEMP" name="TEMP" version="0.1.7"> <description></description> <requirements> <!-- The following are classical toolshed packages and should be removed @@ -19,8 +19,23 @@ <command><![CDATA[ ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && ln -f -s "$alignment" alignment.sorted.bam && - bash $__tool_directory__/scripts/TEMP_Insertion.sh -x "$minimum_score_difference" -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$te_locations" -m "$mismatches" -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && - bash $__tool_directory__/scripts/TEMP_Absence.sh -x "$minimum_score_difference" -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && + bash $__tool_directory__/scripts/TEMP_Insertion.sh + -x "$minimum_score_difference" + -i alignment.sorted.bam + -s $__tool_directory__/scripts + -r "$consensus_te_seqs" + -t "$te_locations" + -m "$mismatches" + -f "$median_insertsize" + -c \${GALAXY_SLOTS:-2} && + bash $__tool_directory__/scripts/TEMP_Absence.sh + -x "$minimum_score_difference" + -i alignment.sorted.bam + -s $__tool_directory__/scripts + -r "$te_locations" + -t "$reference2bit" + -f "$median_insertsize" + -c \${GALAXY_SLOTS:-2} && zip archive.zip *insertion* *excision* *absence* && mv archive.zip $archive && mv alignment.insertion.refined.bp.summary $insertion_summary && mv alignment.absence.refined.bp.summary $absence_summary @@ -30,9 +45,9 @@ <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> <param format="bed" name="te_locations" type="data" label="TE Locations bed file"/> - <param format="txt" name="median_insertsize" type="data" label="Median Insert Length"/> + <param name="median_insertsize" value="" type="integer" label="Median Insert Length"/> <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/> - <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"></param> + <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"/> </inputs> <outputs> <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertion summary file" /> @@ -45,7 +60,7 @@ <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/> <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/> <param name="te_locations" value="test_TE_annotation.gff3" ftype="bed"/> - <param name="median_insertsize" value="median_insert_size" ftype="txt"/> + <param name="median_insertsize" value="500" ftype="integer"/> <output name="insertion_summary" file="test_chromosome.insertion.refined.bp.summary" ftype="bed"/> <output name="absence_summary" file="test_chromosome.absence.refined.bp.summary" ftype="bed"/> </test> @@ -53,14 +68,14 @@ <help> <![CDATA[ +TEMP +------------- TEMP is a software package for detecting transposable elements (TEs) insertions and absences from pooled high-throughput sequencing data Current version v1.04 Author: Jiali Zhuang (jiali.zhuang@umassmed.edu) and Jie Wang (jie.wangj@umassmed.edu) Weng Lab, University of Massachusetts Medical School, Worcester, MA, USA -For TE insertion analysis run TEMP_Insertion.sh in script. -For TE absence analysis run TEMP_Absence.sh in script. Output files -------------