# HG changeset patch
# User devteam
# Date 1487524337 18000
# Node ID d3ae7d9c22023e931ca3fecf17733b106bdbd182
# Parent f1b92120dfaa16dca13ff99dbcf40c9b7153b681
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
diff -r f1b92120dfaa -r d3ae7d9c2202 cuff_macros.xml
--- a/cuff_macros.xml Tue Feb 07 18:39:02 2017 -0500
+++ b/cuff_macros.xml Sun Feb 19 12:12:17 2017 -0500
@@ -8,14 +8,6 @@
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diff -r f1b92120dfaa -r d3ae7d9c2202 cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml Tue Feb 07 18:39:02 2017 -0500
+++ b/cuffdiff_wrapper.xml Sun Feb 19 12:12:17 2017 -0500
@@ -1,14 +1,13 @@
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+find significant changes in transcript expression, splicing, and promoter usecuff_macros.xml
- bioconductor-cummerbund
+ bioconductor-cummerbund
- cuffdiff 2>&1 | head -n 1
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@@ -129,8 +128,8 @@
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@@ -172,16 +171,16 @@
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@@ -265,7 +264,7 @@
@@ -291,7 +290,7 @@
@@ -365,7 +364,7 @@
9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file.
10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here.
11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here.
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**Settings**
@@ -393,7 +392,7 @@
--mask-file (gff3/gtf) Ignore all alignment within transcripts in this file
--time-series Treat provided sam files as time series
--compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.
- --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator
+ --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator
--max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
--num-frag-count-draws Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts.
--num-frag-assign-draws For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts.
diff -r f1b92120dfaa -r d3ae7d9c2202 test-data/cuffdiff_out.sqlite
Binary file test-data/cuffdiff_out.sqlite has changed
diff -r f1b92120dfaa -r d3ae7d9c2202 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Feb 07 18:39:02 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
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- $REPOSITORY_INSTALL_DIR
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