Mercurial > repos > portiahollyoak > temp
diff temp.xml @ 12:ca36262102d8 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
| author | portiahollyoak |
|---|---|
| date | Fri, 29 Apr 2016 05:47:54 -0400 |
| parents | e19d9742c99b |
| children | 72156de89c7a |
line wrap: on
line diff
--- a/temp.xml Thu Apr 28 07:57:12 2016 -0400 +++ b/temp.xml Fri Apr 29 05:47:54 2016 -0400 @@ -1,4 +1,4 @@ -<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2"> +<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.4"> <description></description> <requirements> <!-- The following are classical toolshed packages and should be removed @@ -17,44 +17,35 @@ <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_Insertion.sh -x 30 -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 && + 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} && + 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 && - zip archive.zip *insertion* *excision* *absence* && - mv archive.zip $archive + 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="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> - <param format="bed" name="bed_te_locations" type="data" label="TE Locations bed file"/> - <!-- - <param format="tabular" name="te_families" type="data" label="TE Families"/> - <param format="gff" name="gff_te_locations" type="data" label="Reference TE insertion Locations with Family ID names GFF 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="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> </inputs> <outputs> - <data format="bed" type="data" name="insertion_bed" label="Insertion BED file" /> - <data format="bed" type="data" name="insertion_bed_refined" label="Insertion BED file (refined)" /> <data format="bed" type="data" name="insertion_summary" label="Insertion summary file" /> <data format="bed" type="data" name="absence_summary" label="Absence summary file" /> <data format="zip" type="data" name="archive" label="Compressed output files" /> </outputs> <tests> <test> - <param name="alignment" value="test_chromosome.sorted.bam" ftype="bam"/> - <param name="reference2bit" value="dm3_chr2L.2bit" ftype="twobit"/> + <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/> + <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/> <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/> - <param name="bed_te_locations" value="test_TE_annotation.bed" ftype="bed"/> - <output name="insertion_bed" file="test_chromosome.insertion.bp.bed" ftype="bed" /> - <output name="insertion_bed_refined" file="test_chromosome.insertion.refined.bp" ftype="bed"/> + <param name="te_locations" value="test_TE_annotation.gff3" ftype="bed"/> + <param name="median_insertsize" value="median_insert_size" ftype="txt"/> <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> @@ -71,6 +62,41 @@ For TE insertion analysis run TEMP_Insertion.sh in script. For TE absence analysis run TEMP_Absence.sh in script. +Output files +------------- + + +For TE insertion analysis there are 14 columns in the summary file:: + + 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). + + +For TE absence analysis there are 9 columns in the summary file:: + + 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>