Question: Is && needed in xml for seperating lines?
0
gravatar for 18Kbeyond
4 months ago by
18Kbeyond20
New York
18Kbeyond20 wrote:

Hi. I see an example here https://docs.galaxyproject.org/en/latest/dev/schema.html that && is used to separate two lines:

mkdir -p output_dir &&

python $__tool_directory__/extract_genomic_dna.py

However, when I used && in my xml, it doesn't work - it is not showing up on galaxy when I run run.sh unless I delete &&. So my question is - will this cause a problem ? (Galaxy doesn't give error when I don't add && but the result seems different from what I got from the command line) Is there something to fix in my lines below?

Also the reason I added 2>/dev/null is because bwa aln will print stdout to stderr and galaxy will throw the error message.

#if $seq.method == "singleEnd":

bwa aln -t $nThrds -n $MaxDiff -q $TrimQual ${Ref_fa}.fa $seq.input_query_fq 2>/dev/null > sai &&

bwa samse ${Ref_fa}.fa sai $seq.input_query_fq

#end if

> $output

&& • 134 views
ADD COMMENTlink modified 4 months ago by Devon Ryan1.9k • written 4 months ago by 18Kbeyond20
0
gravatar for Devon Ryan
4 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

&& isn't so much separating lines as it is separating commands. Have a look here for an example using && to separate commands and nothing separating lines (the main command is split across many lines).

If you need help with XML, post the whole relevant bit of code. Note, the code in your post is mixing a things like $variable and ${variable}, which is probably not going to work well.

ADD COMMENTlink written 4 months ago by Devon Ryan1.9k
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