Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

changeset 3:b70047273f38 draft default tip

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef-dirty
author mingchen0919
date Mon, 16 Oct 2017 17:21:26 -0400
parents 58d48d1157ed
children
files fastq_dump_pe.Rmd fastq_dump_pe.xml fastq_dump_se.Rmd fastq_dump_se.xml
diffstat 4 files changed, 16 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dump_pe.Rmd	Mon Oct 16 16:53:21 2017 -0400
+++ b/fastq_dump_pe.Rmd	Mon Oct 16 17:21:26 2017 -0400
@@ -30,7 +30,7 @@
 sra_accessions = sra_accessions[sra_accessions != '']
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
-  if('FORMAT' == 'No') {
+  if('FORMAT' == 'fasta') {
     command = paste0('fastq-dump --fasta --split-files ', '-O read_files_directory ', id)
   } else {
     command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)
--- a/fastq_dump_pe.xml	Mon Oct 16 16:53:21 2017 -0400
+++ b/fastq_dump_pe.xml	Mon Oct 16 17:21:26 2017 -0400
@@ -35,8 +35,10 @@
     <inputs>
         <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false"
                help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
-        <param type="boolean" name="format" truevalue="Yes" falsevalue="No" checked="true"
-               label="output files in fastq (Yes) or fasta (No)?"/>
+        <param type="select" name="format" label="Output format">
+            <option value="fastq" selected="true">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
     </inputs>
--- a/fastq_dump_se.Rmd	Mon Oct 16 16:53:21 2017 -0400
+++ b/fastq_dump_se.Rmd	Mon Oct 16 17:21:26 2017 -0400
@@ -30,7 +30,7 @@
 sra_accessions = sra_accessions[sra_accessions != '']
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
-  if('FORMAT' == 'No') {
+  if('FORMAT' == 'fasta') {
     command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id)
   } else {
     command = paste0('fastq-dump ', '-O read_files_directory ', id)
--- a/fastq_dump_se.xml	Mon Oct 16 16:53:21 2017 -0400
+++ b/fastq_dump_se.xml	Mon Oct 16 17:21:26 2017 -0400
@@ -16,7 +16,7 @@
         <regex match="XXX"
                source="stderr"
                level="warning"
-               description="Check the warnings_and_errors.txt file for more details." />
+               description="Check the warnings_and_errors.txt file for more details."/>
     </stdio>
     <command>
         <![CDATA[
@@ -35,14 +35,18 @@
     <inputs>
         <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions"
                help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
-        <param type="boolean" name="format" truevalue="Yes" falsevalue="No" checked="true" label="output files in fastq (Yes) or fasta (No)?"/>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+        <param type="select" name="format" label="Output format">
+            <option value="fastq" selected="true">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Display analysis code in report?"/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="Fastq-dump report" />
+        <data format="html" name="report" label="Fastq-dump report"/>
         <collection type="list" name="list_collection" label="Fastq-dump (single end reads)">
-            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" />
+            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory"/>
         </collection>
-        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" />
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
     </outputs>
 </tool>
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