# HG changeset patch
# User brasset_jensen
# Date 1527454378 14400
# Node ID b3f0209d3feca3f2360f94e48038565691d38862
# Parent e10a2311e29397999b2a08af4ed603f0b72f2f0b
Uploaded
diff -r e10a2311e293 -r b3f0209d3fec sRNAPipe.xml
--- a/sRNAPipe.xml Sun May 27 16:52:04 2018 -0400
+++ b/sRNAPipe.xml Sun May 27 16:52:58 2018 -0400
@@ -1,236 +1,244 @@
-
- In-depth study of small RNA
-
-
- ./bin/sRNAPipe.pl
-
- --fastq ${first_input}
- --fastq_n ${first_input.name}
- #for $input_file in $input_files:
- --fastq ${input_file.additional_input}
- --fastq_n ${input_file.additional_input.name}
- #end for
-
- #if $Genome.refGenomeSource == "history":
- --ref "${Genome.ownFile}"
- --build_index
- #else:
- --ref "${Genome.indices.fields.path}"
- #end if
-
- #if $tRNAs.refGenomeSource == "history":
- --tRNAs "${tRNAs.ownFile}"
- --build_tRNAs
- #elif $tRNAs.refGenomeSource == "none":
- --tRNAs "None"
- #else:
- --tRNAs "${tRNAs.indices.fields.path}"
- #end if
-
- #if $snRNAs.refGenomeSource == "history":
- --snRNAs "${snRNAs.ownFile}"
- --build_snRNAs
- #elif $snRNAs.refGenomeSource == "none":
- --snRNAs "None"
- #else:
- --snRNAs "${snRNAs.indices.fields.path}"
- #end if
-
- #if $rRNAs.refGenomeSource == "history":
- --rRNAs "${rRNAs.ownFile}"
- --build_rRNAs
- #elif $rRNAs.refGenomeSource == "none":
- --rRNAs "None"
- #else:
- --rRNAs "${rRNAs.indices.fields.path}"
- #end if
-
- #if $miRNAs.refGenomeSource == "history":
- --miRNAs "${miRNAs.ownFile}"
- --build_miRNAs
- #else:
- --miRNAs "${miRNAs.indices.fields.path}"
- #end if
-
- #if $transcripts.refGenomeSource == "history":
- --transcripts "${transcripts.ownFile}"
- --build_transcripts
- #else:
- --transcripts "${transcripts.indices.fields.path}"
- #end if
-
- #if $TE.refGenomeSource == "history":
- --TE "${TE.ownFile}"
- --build_TE
- #else:
- --TE "${TE.indices.fields.path}"
- #end if
-
- --si_min $si_min
- --si_max $si_max
- --pi_min $pi_min
- --pi_max $pi_max
- --min $min
- --max $max
-
- --mis $mis
- --misTE $misTE
- --dir $html_out.files_path
- --html $html_out
- --PPPon $PPPon
-
-
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- bwa
- bedtools
- samtools
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+
+ In-depth study of small RNA
+
+
+ ./bin/sRNAPipe.pl
+
+ --fastq ${first_input}
+ --fastq_n ${first_input.name}
+ #for $input_file in $input_files:
+ --fastq ${input_file.additional_input}
+ --fastq_n ${input_file.additional_input.name}
+ #end for
+
+ #if $Genome.refGenomeSource == "history":
+ --ref "${Genome.ownFile}"
+ --build_index
+ #else:
+ --ref "${Genome.indices.fields.path}"
+ #end if
+
+ #if $tRNAs.refGenomeSource == "history":
+ --tRNAs "${tRNAs.ownFile}"
+ --build_tRNAs
+ #elif $tRNAs.refGenomeSource == "none":
+ --tRNAs "None"
+ #else:
+ --tRNAs "${tRNAs.indices.fields.path}"
+ #end if
+
+ #if $snRNAs.refGenomeSource == "history":
+ --snRNAs "${snRNAs.ownFile}"
+ --build_snRNAs
+ #elif $snRNAs.refGenomeSource == "none":
+ --snRNAs "None"
+ #else:
+ --snRNAs "${snRNAs.indices.fields.path}"
+ #end if
+
+ #if $rRNAs.refGenomeSource == "history":
+ --rRNAs "${rRNAs.ownFile}"
+ --build_rRNAs
+ #elif $rRNAs.refGenomeSource == "none":
+ --rRNAs "None"
+ #else:
+ --rRNAs "${rRNAs.indices.fields.path}"
+ #end if
+
+ #if $miRNAs.refGenomeSource == "history":
+ --miRNAs "${miRNAs.ownFile}"
+ --build_miRNAs
+ #else:
+ --miRNAs "${miRNAs.indices.fields.path}"
+ #end if
+
+ #if $transcripts.refGenomeSource == "history":
+ --transcripts "${transcripts.ownFile}"
+ --build_transcripts
+ #else:
+ --transcripts "${transcripts.indices.fields.path}"
+ #end if
+
+ #if $TE.refGenomeSource == "history":
+ --TE "${TE.ownFile}"
+ --build_TE
+ #else:
+ --TE "${TE.indices.fields.path}"
+ #end if
+
+ --si_min $si_min
+ --si_max $si_max
+ --pi_min $pi_min
+ --pi_max $pi_max
+ --min $min
+ --max $max
+
+ --mis $mis
+ --misTE $misTE
+ --dir $html_out.files_path
+ --html $html_out
+ --PPPon $PPPon
+
+
+
+ bwa
+ bedtools
+ samtools
+
+
+
+
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