Mercurial > repos > portiahollyoak > temp
diff temp_absences.xml @ 21:9672fe07a232 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author | mvdbeek |
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date | Mon, 05 Dec 2016 09:58:47 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/temp_absences.xml Mon Dec 05 09:58:47 2016 -0500 @@ -0,0 +1,103 @@ +<tool id ="TEMP_absences" name="TEMP Excision" version="0.3.0"> + <description>finds TEs that have excised relative to the reference</description> + <requirements> + <requirement type="package" version="1.6.924=pl5.22.0_0">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="1.3.1">samtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && + ln -f -s "$alignment" alignment.sorted.bam && + bash $__tool_directory__/scripts/TEMP_Absence.sh + -x "$minimum_score_difference" + -i alignment.sorted.bam + -s $__tool_directory__/scripts + -r "$te_locations" + -t "$reference2bit" + -f "$median_insertsize" + -c \${GALAXY_SLOTS:-2} && + mv alignment.absence.refined.bp.summary $absence_summary + ]]></command> + <inputs> + <param format="bam" name="alignment" type="data" label="Alignment bam file"/> + <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> + <param format="bed" name="te_locations" type="data" label="TE Annotations bed file"/> + <param name="median_insertsize" value="" type="integer" label="Median Insert Length"/> + <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum difference between mapping scores"/> + </inputs> + <outputs> + <data format="bed" name="absence_summary" label="${alignment.element_identifier} Absences" /> + </outputs> + <tests> + <test> + <param name="alignment" value="test_chromosome.sorted.bam" ftype="bam"/> + <param name="reference2bit" value="dm3_chr2L.2bit" ftype="twobit"/> + <param name="te_locations" value="test_TE_annotation.bed" ftype="bed"/> + <param name="median_insertsize" value="500" ftype="integer"/> + <output name="absence_summary" file="test_absence_out.bed" ftype="bed"/> + </test> + </tests> + <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 + +*Input files/variables* +------------------------- +* Alignment file in BAM format +* Reference genome used in aligning, in fasta or twobit format. +* Transposable Elements' Consensus Sequences in fasta format. +* Annotations of TEs in reference genome in bed format. +* TE Identifiers and Families (optional) - A file containing in the first column the TE names/identifiers from the consensus sequences file, and in the second column, their respective TE family names as in the TE annotations file. When supplied, if a detected insertion overlaps with an annotated TE of the same family, the detected insertion will be excluded from the results. +* Median Insert Length +* Number of Mismatches allowed (default 3) +* Minimum difference between mapping scores. The minimum difference in scores between the optimal and suboptimal alignments to consider a read uniquely mapped. + +*Output files* +----------------- +* **In the Insertions output file there are 14 columns:** +* Column 1: The chromosome where the detected insertion happens. +* Column 2: The coordinate of the start position of the detected insertion. +* Column 3: The coordinate of the end position of the detected insertion. +* Column 4: The TE family that the detected insertion belongs to. +* Column 5: The direction of the insertion. “Plus” means that the TE is integrated with the plus strand of the genome while “minus” means the TE is integrated with the minus strand. +* Column 6: The class of the insertion. “1p1” means that the detected insertion is supported by reads at both sides. “2p” means the detected insertion is supported by more than 1 read at only 1 side. “Singleton” means the detected insertion is supported by only 1 read at 1 side. +* Column 7: The total number of read pairs that support the detected insertion. +* Column 8: The estimated population frequency of the detected insertion. +* Columns 9 & 10: The coordinate of a junction and the number of the reads supporting it. If the junction is not found column 9 will be the arithmetic mean of the start and end coordinates and column 10 will have the value 0. +* Columns 11 & 12: Same as Columns 9 & 10 except for the junction on the other strand. +* Column 13: The number of reads supporting the detected insertion at the 5’ end of the TE (not including junction spanning reads). +* Column 13: The number of reads supporting the detected insertion at the 3’ end of the TE (not including junction spanning reads). + + +----- + + +* **In the Absences output file there are 14 columns:** +* Column 1: The chromosome where the detected absence happens. +* Column 2: The coordinate of the start position of the detected absence. +* Column 3: The coordinate of the end position of the detected absence. +* Column 4: The TE family that the detected insertion belongs to. +* Column 5: Junctions at 5’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands. +* Column 6: Junctions at 3’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands. +* Column 7: The number of reads supporting the absence. +* Column 8: The number of reads supporting the reference (no absence). +* Column 9: Estimated population frequency of the detected absence event. + + + ]]> </help> + <citations> + <citation type="doi">10.1093/nar/gku323</citation> + </citations> +</tool>