diff fastq_dump_se.xml @ 0:7ec600e7dba7 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_dump_se.xml	Wed Sep 27 09:25:48 2017 -0400
@@ -0,0 +1,52 @@
+<tool id="rmarkdown_fastqc_dump" name="fastqc-dump" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+        <requirement type="package" version="0.5.0">r-dplyr</requirement>
+        <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
+    </requirements>
+    <description>
+        Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets
+        collection.
+    </description>
+    <stdio>
+        <regex match="Execution halted"
+               source="both"
+               level="fatal"
+               description="Execution halted." />
+        <regex match="Error in"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+        <regex match="Fatal error"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
+    <command>
+        <![CDATA[
+            Rscript '${__tool_directory__}/fastqc_dump_se_render.R'
+                -i $sra_accession
+                -e $echo
+                -f $format
+
+                -r $report
+                -d $report.files_path
+
+                -t '${__tool_directory__}/fastq_dump_se.Rmd'
+        ]]>
+    </command>
+    <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="fastq" falsevalue="fasta" checked="false" label="output files in fastq (true) or fasta (false)?"/>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <collection type="list" name="list_collection">
+            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" />
+        </collection>
+    </outputs>
+</tool>
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