Dear Matthias,

Yes, you can define number of outputs dynamically in Galaxy. For doing this, you'll have to declare one output dataset in your xml and pass its ID ($out_file.id) to your python script. Also, set force_history_refresh="True" in your tool tag in xml, like this: <tool id="split1" name="Split" force_history_refresh="True"> In your script, if your outputs are named in the following format, primary_associatedWithDatasetID_designation_visibility_extension (_DBKEY), all your datasets will show up in the history pane. associatedWithDatasetID is the $out_file.ID passed from xml, designation will be a unique identifier for each output (set in your script), visibility can be set to visible if you want the dataset visible in your history, or notvisible otherwise extension is the required format for your dataset (bed, tabular, fasta etc) DBKEY is optional, and can be set if required (e.g. hg18, mm9 etc)

One of our tools "MAF to Interval converter" (tools/maf/ maf_to_interval.xml) already uses this feature. You can use it as a reference.

Hope this answers your question. Please feel free to email us if you have any more queries. Guru Galaxy team.

On Sep 29, 2009, at 9:52 AM, Matthias Dodt wrote:

Hi galaxy-users!

I wrote a tool that splits a FASTA file into n output files, each one of a predefined maximum size. The program could return the number of files or a list of filenames...

Is it possible to define the number of outputs dynamically (nr of output files dependent on input-filesize)?

Thanks!

till now i experimented with:

<tool id="seqan_splitter_1" name="FASTA splitter"> <description>Splits input files into pieces of desired size</ description> <command interpreter="python"> ./tools/RNA-seq/fasta-splitter/fasta-splitter.py --maxsize $size 2> $log_report </command>

<inputs> <param name="source" type="data" format="fasta" label="input fasta file"/> <param name="size" type="integer" label="Size in Megabyte of each output file" value="500" optional="false"/> <param name="files" type="hidden" value="10"/> </inputs>

<outputs> #for $i < $files <data format="fasta" name="\$i" label="Splitted file"/> #end for <data format="text" name="log_report" label="Detailed log report from splitter"/> </outputs>

</tool>

---

galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

Regards,

Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

Hi,

how does/could this work in the workflow creation. How should/can I redirect all created outputs to a new tool which also accepts a dynamical number of inputs?

Cheers, Jelle

2009/10/1 Matthias Dodt matthias.dodt@mdc-berlin.de

Hi Guru!

Thank you very much for the detailed reply! - now it works. Just one thing is strange: In the history appear the double amount of files, half of them has size zero and contains actually nothing. I wrote a program which splits a fasta/fastq file into n files. On the command line it works fine (the names of the output files can be specified directly via parameter). However there are always 2n files of the history - half of them empty. Any idea?

the xml-file looks as follows: <tool id="seqan_splitter_1" name="FASTA splitter" force_history_refresh="True"> <description>Splits input files into pieces of desired size</description>

<command> ./tools/RNA-seq/fasta-splitter/seqan_splitter --source $source --name-pattern primary_${resultset.id}_splitfile%_visible_fasta --target-dir $__new_file_path__/ --maxsize $size #if $format_input.type =="fasta" --format fasta #else --format fastq #end if > /dev/null ##2> $log_report </command>

<inputs> <conditional name="format_input"> <param name="type" type="select" label="input file format" optional="false"> <option value="fasta" selected="true">FASTA</option> <option value="fastqsanger">FASTQSanger</option> <option value="fastqsolexa">FASTQSolexa</option> </param> <when value="fasta"> <param format="fasta" name="source" type="data" label="source file"/> </when> <when value="fastqsolexa"> <param format="fastqsolexa" name="source" type="data" label="source file"/> </when> <when value="fastqsanger"> <param format="fastqsanger" name="source" type="data" label="source file"/> </when> </conditional> <param name="size" type="integer" label="Size in Megabyte of each output file" value="500" optional="false"/> </inputs>

<outputs> <data format="fasta" name="resultset" label="Splitted file"/> <!-- <data format="text" name="log_report" label="Detailed log report from splitter"/>--> </outputs>

<help> </help> </tool>

Thanks again!

greetings

mat

Guruprasad Ananda schrieb:

...

Dear Matthias,

Yes, you can define number of outputs dynamically in Galaxy. For doing this, you'll have to declare one output dataset in your xml and pass its ID ($out_file.id) to your python script. Also, set force_history_refresh="True" in your tool tag in xml, like this:

<tool id="split1" name="Split" force_history_refresh="True"> In your script, if your outputs are named in the following format, primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY), all your datasets will show up in the history pane. associatedWithDatasetID is the $out_file.ID passed from xml, designation will be a unique identifier for each output (set in your script), visibility can be set to visible if you want the dataset visible in your history, or notvisible otherwise extension is the required format for your dataset (bed, tabular, fasta etc) DBKEY is optional, and can be set if required (e.g. hg18, mm9 etc)

One of our tools "MAF to Interval converter" (tools/maf/maf_to_interval.xml) already uses this feature. You can use it as a reference.

Hope this answers your question. Please feel free to email us if you have any more queries. Guru Galaxy team.

On Sep 29, 2009, at 9:52 AM, Matthias Dodt wrote:

...

Hi galaxy-users!

I wrote a tool that splits a FASTA file into n output files, each one of a predefined maximum size. The program could return the number of files or a list of filenames...

Is it possible to define the number of outputs dynamically (nr of output files dependent on input-filesize)?

Thanks!

till now i experimented with:

<tool id="seqan_splitter_1" name="FASTA splitter"> <description>Splits input files into pieces of desired size</description> <command interpreter="python"> ./tools/RNA-seq/fasta-splitter/fasta-splitter.py --maxsize $size 2> $log_report </command>

<inputs> <param name="source" type="data" format="fasta" label="input fasta file"/> <param name="size" type="integer" label="Size in Megabyte of each output file" value="500" optional="false"/> <param name="files" type="hidden" value="10"/> </inputs>

<outputs> #for $i < $files <data format="fasta" name="\$i" label="Splitted file"/> #end for <data format="text" name="log_report" label="Detailed log report from splitter"/> </outputs>

</tool>

---

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Regards,

Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

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