I double check the output format of "Select Variants", which is in VCF. For the input of SnpEff, it is also in VCF. I do not know why can not I construct a connection between them. The most strange thing is that I could not re-build the connection when I deleted the original one in the workflow. Thanks a lot! ________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfwang@ku.edu] Sent: Monday, April 14, 2014 2:35 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] how to edit the workflow (the connection between Select Variants and SnpEff) Dear there, I tried to edit the CloudMap EMS workflow based on my own data. But I failed to make a connection between "Select Variants" and "SnpEff". In fact, I failed to reconstruct the connection between them even when I removed the original one by clicking "x" when moved cursor on the line. The arrow on left of SnpEff does not become green when I drugged the line from output_vcf(vcf) to it after I moved the original one. Could you tell me why does this happen and how should I figure this out? [cid:d1b6886a-ce80-e25c-2ede-e7afbe43263c] Thanks a lot! Best Xiaofei

Long story short - there is a typo in the older version of this snpeff tool on usegalaxy.org. Newer versions of the snpeff tool do not seem to contain this typo - I don't know if there are plans to upgrade the tool on usegalaxy.org. For more technical details - its input to this older version of the tool is labelled as "Tabular" instead of "tabular". The tool processing pieces of Galaxy will default to treating this unknown type as "data" and so match anything to it but the workflow editor takes the extension at face value and decides nothing with an explicit output type can connect to it. -John On Wed, Apr 16, 2014 at 9:37 AM, Wang, Xiaofei <xfwang@ku.edu> wrote:

Dear there,

Could someone help me figure this out? Thank you so much! Why could not I build a connection between Select Variants and SnpEff?

Best,

Xiaofei ------------------------------ *From:* Wang, Xiaofei *Sent:* Tuesday, April 15, 2014 9:39 AM *To:* galaxy-dev@lists.bx.psu.edu *Subject:* RE: [galaxy-dev] how to edit the workflow (the connection between Select Variants and SnpEff)

I double check the output format of "Select Variants", which is in VCF. For the input of SnpEff, it is also in VCF. I do not know why can not I construct a connection between them. The most strange thing is that I could not re-build the connection when I deleted the original one in the workflow. Thanks a lot! ------------------------------ *From:* galaxy-dev-bounces@lists.bx.psu.edu [ galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Wang, Xiaofei [ xfwang@ku.edu] *Sent:* Monday, April 14, 2014 2:35 PM *To:* galaxy-dev@lists.bx.psu.edu *Subject:* [galaxy-dev] how to edit the workflow (the connection between Select Variants and SnpEff)

Dear there,

I tried to edit the CloudMap EMS workflow based on my own data. But I failed to make a connection between "Select Variants" and "SnpEff". In fact, I failed to reconstruct the connection between them even when I removed the original one by clicking "x" when moved cursor on the line. The arrow on left of SnpEff does not become green when I drugged the line from output_vcf(vcf) to it after I moved the original one. Could you tell me why does this happen and how should I figure this out?

Thanks a lot!

Best

Xiaofei

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