# HG changeset patch
# User portiahollyoak
# Date 1466001006 14400
# Node ID e7d3dc3e0ec937eee657f893eea31591c294aa84
# Parent  c613f8c96e6d117d3bce7959957ba5b00814ec0b
planemo upload for repository https://github.com/portiahollyoak/Tools commit 22724a75342e3097cd0976e4bfcfe7a19308ac4f-dirty

diff -r c613f8c96e6d -r e7d3dc3e0ec9 scripts/TEMP_Insertion.sh
--- a/scripts/TEMP_Insertion.sh	Tue Jun 14 04:36:25 2016 -0400
+++ b/scripts/TEMP_Insertion.sh	Wed Jun 15 10:30:06 2016 -0400
@@ -156,6 +156,7 @@
 rm tmp
 perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed
 perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI
+echo "got FAMI"
 
 rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai 
 rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed
diff -r c613f8c96e6d -r e7d3dc3e0ec9 scripts/families
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/families	Wed Jun 15 10:30:06 2016 -0400
@@ -0,0 +1,5556 @@
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diff -r c613f8c96e6d -r e7d3dc3e0ec9 scripts/fbtis
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/fbtis	Wed Jun 15 10:30:06 2016 -0400
@@ -0,0 +1,5556 @@
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+RR48358_transposable_element
+FBti0019747
+FBti0061779
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+FBti0061944
+FBti0062347
+FBti0061945
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+FBti0061946
+FBti0062414
+FBti0061947
+RR48316_transposable_element
+RR43222_transposable_element
+RR48361_transposable_element
+RR43316_transposable_element
+RR48328_transposable_element
+RR48365_transposable_element
+RR48308_transposable_element
+RR48330_transposable_element
+RR45003_transposable_element
diff -r c613f8c96e6d -r e7d3dc3e0ec9 temp.xml
--- a/temp.xml	Tue Jun 14 04:36:25 2016 -0400
+++ b/temp.xml	Wed Jun 15 10:30:06 2016 -0400
@@ -1,4 +1,4 @@
-<tool id ="run_TEMP" name="TEMP" version="0.1.8">
+<tool id ="run_TEMP" name="TEMP" version="0.2.0">
     <description></description>
     <requirements>
         <!-- The following are classical toolshed packages and should be removed
@@ -25,6 +25,9 @@
         -s $__tool_directory__/scripts
         -r "$consensus_te_seqs"
         -t "$te_locations"
+        #if $te_families:
+        -u "$te_families"
+        #end if
         -m "$mismatches"
         -f "$median_insertsize"
         -c \${GALAXY_SLOTS:-2} &&
@@ -44,10 +47,11 @@
         <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="te_locations" type="data" label="TE Locations bed file"/>
+        <param format="bed" name="te_locations" type="data" label="TE Annotations bed file"/>
+        <param format="tabular" name="te_families" type="data" optional="True" label="TE Identifiers and Families"/>
         <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 name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum difference between mapping scores"/>
     </inputs>
     <outputs>
         <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" />
@@ -76,38 +80,47 @@
 
 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
--------------
+*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).
 
 
-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.
+* **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>