# HG changeset patch
# User bgruening
# Date 1568041882 14400
# Node ID 4de6e2e40c7a529c076a3a443bd2ffd747270640
# Parent 2c0ca397d3025a740e49123b5b3b891023fb6092
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
diff -r 2c0ca397d302 -r 4de6e2e40c7a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Sep 09 11:11:22 2019 -0400
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+
+ 0.14.1
+ galaxy0
+ q5
+
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+ bzip2
+ seqtk
+ salmon
+ samtools
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+ 10.1186/s13059-019-1670-y
+ 10.1038/nmeth.4197
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+ `__ and `Salmon `__ wikis.
+ ]]>
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diff -r 2c0ca397d302 -r 4de6e2e40c7a salmon.xml
--- a/salmon.xml Sat Jul 27 12:37:47 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,885 +0,0 @@
-
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- Transcript Quantification from RNA-seq data
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- 0.11.2
- q5
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- bzip2
- salmon
- seqtk
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- salmon -version
- ${output_sam}
- #end if
-]]>
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- geneMap
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- adv['writeMappings']
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- `_ RNA-seq
- read aligner has a different convention for specifying the format of the library.
- Below is a table that provides the corresponding Salmon/salmon library format
- string for each of the potential TopHat library types:
-
- +---------------------+-------------------------+
- | TopHat | Salmon (and Sailfish) |
- +=====================+============+============+
- | | Paired-end | Single-end |
- +---------------------+------------+------------+
- |``-fr-unstranded`` |``-l IU`` |``-l U`` |
- +---------------------+------------+------------+
- |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |
- +---------------------+------------+------------+
- |``-fr-secondstrand`` |``-l ISF`` |``-l SF`` |
- +---------------------+------------+------------+
-
- The remaining salmon library format strings are not directly expressible in terms
- of the TopHat library types, and so there is no direct mapping for them.
-]]>
-
- 10.1101/021592
-
-
diff -r 2c0ca397d302 -r 4de6e2e40c7a salmonquant.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/salmonquant.xml Mon Sep 09 11:11:22 2019 -0400
@@ -0,0 +1,267 @@
+
+ Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads
+
+ macros.xml
+
+
+ ./output/bamout.bam
+ #end if
+ #end if
+ #if $quant_type.qtype == "alignment":
+ #if $quant_type.sampleOut:
+ && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam
+ #end if
+ #end if
+ ]]>
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+ geneMap
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+ quant_type['qtype'] == "reads" and quant_type['writeMappings']
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+ quant_type['qtype'] == "alignment" and quant_type['sampleOut']
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