Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 47:fb05ca474127 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit a7ad932a1725b4ef26d522040c5395ae0026fb35-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 26 Sep 2017 12:24:21 -0400 |
| parents | 8dacd341b8b7 |
| children | 68da32dbc6e2 |
| files | collection_list_paired.xml collection_paired.xml collection_paired_render.R |
| diffstat | 3 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/collection_list_paired.xml Tue Sep 26 12:10:20 2017 -0400 +++ b/collection_list_paired.xml Tue Sep 26 12:24:21 2017 -0400 @@ -40,7 +40,7 @@ <inputs> <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/> <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/> - <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> + <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> </inputs>
--- a/collection_paired.xml Tue Sep 26 12:10:20 2017 -0400 +++ b/collection_paired.xml Tue Sep 26 12:24:21 2017 -0400 @@ -38,8 +38,8 @@ ]]> </command> <inputs> - <param type="data" name="forward_input" multiple="true" label="forward input"/> - <param type="data" name="reverse_input" multiple="true" label="reverse input"/> + <param type="data" name="forward_input" multiple="false" label="forward input"/> + <param type="data" name="reverse_input" multiple="false" label="reverse input"/> <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
--- a/collection_paired_render.R Tue Sep 26 12:10:20 2017 -0400 +++ b/collection_paired_render.R Tue Sep 26 12:24:21 2017 -0400 @@ -31,14 +31,14 @@ ##------- 1. input data --------------------- spec_list=list() spec_list$FORWARD_INPUT = c('forward_input', 'L', '1', 'character') -spec_list$REVERSE_INPUT = c('reverse_forward_input', 'R', '1', 'character') +spec_list$REVERSE_INPUT = c('reverse_input', 'R', '1', 'character') spec_list$ECHO = c('echo', 'e', '1', 'character') spec_list$FORMAT = c('format', 'f', '1', 'character') ##--------2. output report and outputs -------------- spec_list$OUTPUT_HTML = c('paired_collection_html', 'r', '1', 'character') spec_list$OUTPUT_DIR = c('paired_collection_dir', 'd', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- -spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') +spec_list$PAIRED_COLLECTION_RMD = c('paired_collection_rmd', 't', '1', 'character') spec = t(as.data.frame(spec_list)) opt = getopt(spec) @@ -58,8 +58,8 @@ # b. templates with placeholder variables: # substitute variables with user input values and place them in the working directory. -#----- 01 list_collection.Rmd ----------------------- -readLines(opt$list_collection_rmd) %>% +#----- 01 paired_collection.Rmd ----------------------- +readLines(opt$paired_collection_rmd) %>% (function(x) { gsub('ECHO', opt$echo, x) }) %>%