Mercurial > repos > refinery-platform > emsar
changeset 0:41e92972b7f1 draft default tip
Fix XML formatting
| author | refinery-platform |
|---|---|
| date | Wed, 02 Sep 2015 16:37:50 -0400 |
| parents | |
| children | |
| files | emsar_indices.loc.sample emsar_wrapper.xml tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 102 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emsar_indices.loc.sample Wed Sep 02 16:37:50 2015 -0400 @@ -0,0 +1,5 @@ +# EMSAR rsh files +# +# format of this .loc file (5 tab-separated columns): +#value dbkey description path to index? path to rsh file +#hg19 hg19 Human (hg19) ~/refs/hg19/EMSAR/RefSeq_hg19 ~/refs/hg19/EMSAR/rsh/RefSeq.hg19.PE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emsar_wrapper.xml Wed Sep 02 16:37:50 2015 -0400 @@ -0,0 +1,91 @@ +<tool id="emsar" name="EMSAR" version="1.2j"> + <description></description> + + <command> + + #set rsh_path = $refIndex.fields.rshPath + #set rsh = $rsh_path + "." + $nRL.__str__() + ".rsh" + #set libType = "" + + #if $bPaired + #if $sLT.__str__() == "n" + #set libType = "ns" + #end if + #if $sLT.__str__() == "f" + #set libType = "ssfr" + #end if + #if $sLT.__str__() == "r" + #set libType = "ssrf" + #end if + #else + #if $sLT.__str__() == "n" + #set libType = "ns" + #end if + #if $sLT.__str__() == "f" + #set libType = "ssf" + #end if + #if $sLT.__str__() == "r" + #set libType = "ssr" + #end if + #end if + + emsar + -P + #if $sBS.__str__() == "S" + -S + #end if + #if $sBS.__str__() == "B" + -B + #end if + -p 8 + -h $sHT + #if $bG + -g + #end if + -s $libType + -I $rsh + output + emsar + $input_bam + 2> emsar.log + + </command> + + <stdio></stdio> + + <inputs> + <param format="bam,sam" compression="none" name="input_bam" type="data" label="Bowtie Alignment BAM file" help=""/> + <param name="refIndex" type="select" label="Select a reference genome" help=""> + <options from_data_table="emsar_indices"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No genomes are available for the selected input dataset"/> + </options> + </param> + <param name="sBS" type="select" label="Input alignment file type "> + <option value="S">SAM</option> + <option value="B">BAM</option> + </param> + <param name="sHT" type="select" label="Transcriptome header type"> + <option value="R">RefSeq</option> + <option value="E">Ensembl</option> + </param> + <param name="bG" type="boolean" label="Generate list of all segments with their associated sequence-sharing set and transcript(seperated by '+')" value="True" /> + <param name="bPaired" type="boolean" label="Is this paired-end sequenced data ?" value="True" /> + <param name="nRL" type="integer" label="read length" value="101" /> + <param name="sLT" type="select" label="library type"> + <option value="n">Unstranded</option> + <option value="f">Forward Stranded</option> + <option value="r">Reverse Stranded</option> + </param> + </inputs> + + <outputs> + <data format="txt" name="fpkm" label="${tool.name} on ${on_string}: FPKM" from_work_dir="output/emsar.0.fpkm" /> + <data format="txt" name="fraglength_stat" label="${tool.name} on ${on_string}: Fracgment Length Effect" from_work_dir="output/emsar.0.fraglength_effect" /> + <data format="txt" name="segments" label="${tool.name} on ${on_string}: Segments" from_work_dir="output/emsar.0.segments" /> + </outputs> + + <help> + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Sep 02 16:37:50 2015 -0400 @@ -0,0 +1,6 @@ +<tables> + <table name="emsar_indices" comment_char="#"> + <columns>value, dbkey, name, idxPath, rshPath</columns> + <file path="emsar_indices.loc" /> + </table> +</tables>