optional tool arguments
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: <tool id="subsample_fastq" name="Random subsample"> <description>a fastq file</description> <command> ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if </command> <inputs> <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/> <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/> <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/> </inputs> <outputs> <data format="fastq" name="out1" /> <data format="fastq" name="out2" /> </outputs> <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>
Hi Ryan I guess you can work with filters, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_... Regards, Hans-Rudolf On 04/28/2015 06:28 PM, Ryan G wrote:
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter?
I'm using this as my tool description right now:
<tool id="subsample_fastq" name="Random subsample"> <description>a fastq file</description> <command> ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if </command> <inputs> <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/> <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/> <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/> </inputs> <outputs> <data format="fastq" name="out1" /> <data format="fastq" name="out2" /> </outputs> <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>
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Yes, for example: https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/se... Peter On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Ryan
I guess you can work with filters, see:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_...
Regards, Hans-Rudolf
On 04/28/2015 06:28 PM, Ryan G wrote:
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter?
I'm using this as my tool description right now:
<tool id="subsample_fastq" name="Random subsample"> <description>a fastq file</description> <command> ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if </command> <inputs> <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/> <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/> <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/> </inputs> <outputs> <data format="fastq" name="out1" /> <data format="fastq" name="out2" /> </outputs> <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>
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Yes it took some experimenting but I finally figured it out. Sent from my iPhone
On Apr 29, 2015, at 4:51 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Yes, for example: https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/se...
Peter
On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote: Hi Ryan
I guess you can work with filters, see:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_...
Regards, Hans-Rudolf
On 04/28/2015 06:28 PM, Ryan G wrote:
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter?
I'm using this as my tool description right now:
<tool id="subsample_fastq" name="Random subsample"> <description>a fastq file</description> <command> ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if </command> <inputs> <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/> <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/> <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/> </inputs> <outputs> <data format="fastq" name="out1" /> <data format="fastq" name="out2" /> </outputs> <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
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Hans-Rudolf Hotz -
Peter Cock -
Ryan G