Mercurial > repos > mingchen0919 > aurora_dustmasker
changeset 1:e0828838e0f3 draft default tip
update
author | mingchen0919 |
---|---|
date | Fri, 09 Nov 2018 15:25:01 -0500 |
parents | b8c76b06d724 |
children | |
files | galaxy_outputs.sh rmarkdown_report.Rmd rmarkdown_report.xml scripts_generator.sh |
diffstat | 4 files changed, 47 insertions(+), 26 deletions(-) [+] |
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--- a/galaxy_outputs.sh Fri Nov 09 13:29:21 2018 -0500 +++ b/galaxy_outputs.sh Fri Nov 09 15:25:01 2018 -0500 @@ -10,6 +10,6 @@ cp index.html ${REPORT} fi -if [ -e "dustmasker_out" ]; then - cp dustmasker_out $X_H +if [ -e "masked_file.txt" ]; then + cp masked_file.txt $X_H fi
--- a/rmarkdown_report.Rmd Fri Nov 09 13:29:21 2018 -0500 +++ b/rmarkdown_report.Rmd Fri Nov 09 15:25:01 2018 -0500 @@ -1,5 +1,5 @@ --- -title: 'Aurora Tool Report' +title: 'Dustmasker Report' output: html_document: highlight: pygments @@ -54,23 +54,21 @@ --- -## Run `dustmasker` +## Run `dustmasker` job -```{bash} -dustmasker \ - -in $X_A \ - -window $X_B \ - -level $X_C \ - -linker $X_D \ - -infmt $X_E \ - -outfmt $X_F \ - - $(if [ "$X_G" = "NO_ARGUMENT_YES" ]; then echo '-parse_seqids'; fi) \ - - -out dustmasker_out +```{bash echo=FALSE} +sh ${TOOL_INSTALL_DIR}/scripts_generator.sh ``` -Options explanation: +```{r echo=FALSE,warning=FALSE,results='asis'} +# display content of the job-script.sh file. +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/dustmasker.sh')), sep = '\n') +cat('\n```') +``` + + +**Options explanation:** <pre> -in <File_In> @@ -98,5 +96,4 @@ -out <File_Out> output file name - Default = `-' </pre> \ No newline at end of file
--- a/rmarkdown_report.xml Fri Nov 09 13:29:21 2018 -0500 +++ b/rmarkdown_report.xml Fri Nov 09 15:25:01 2018 -0500 @@ -23,20 +23,21 @@ -d $report.files_path -A $input_fasta - -B $level - -C $linker - -D $input_format - -E $output_format - -F $parse_seqids + -B $window_length + -C $level + -D $linker + -E $input_format + -F $output_format + -G $parse_seqids - -G $out + -H $out ]]></command> <inputs> - <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="input_format_fasta" selected="true">fasta</option><option value="input_format_blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="output_acclist" selected="false">acclist</option><option value="output_fasta" selected="false">fasta</option><option value="output_interval" selected="false">interval</option><option value="output_maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="output_maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="output_maskinfo_xml" selected="false">maskinfo_xml</option><option value="output_seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="output_seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="output_seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs> + <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="fasta" selected="true">fasta</option><option value="blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="acclist" selected="false">acclist</option><option value="fasta" selected="true">fasta</option><option value="interval" selected="false">interval</option><option value="maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="maskinfo_xml" selected="false">maskinfo_xml</option><option value="seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs> <outputs> - <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" label="${tool.name} on ${on_string}" hidden="false"/></outputs> + <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" format="fasta" label="${tool.name} on ${on_string}" hidden="false"/></outputs> <citations> <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts_generator.sh Fri Nov 09 15:25:01 2018 -0500 @@ -0,0 +1,23 @@ +# run SHELL_SCRIPT within tool outputs directory +cd ${REPORT_FILES_PATH} + + +# generate dustmasker.sh script +cat >temp.sh <<EOF +dustmasker \\ + -in ${X_A} \\ + -window ${X_B} \\ + -level ${X_C} \\ + -linker ${X_D} \\ + -infmt ${X_E} \\ + -outfmt ${X_F} \\ + -parse_seqids ${X_G} \\ + -out masked_file.txt > dustmasker.log.txt 2>&1 + +EOF + +grep -v 'NO_ARGUMENT_NO' temp.sh > dustmasker.sh +rm temp.sh + +# run dustmasker job +sh dustmasker.sh \ No newline at end of file