Hi everyone, I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ? Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ? An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ? thx, Jerome
On Mon, Jun 6, 2011 at 2:45 PM, Mariette <jmariett@toulouse.inra.fr> wrote:
Hi everyone,
I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ?
I use a wrapper script which moves the output file from the sub-directory to the location Galaxy requested. Regarding the file format, if you only have one input file you can use format="input", otherwise use the change_format tag in the XML.
Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ?
An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ?
Normally the wrapper specifies the output format explicitly. Peter
Thanks for the answer, so I tryed to write a wrapper, but the main script is not recognize. When I'm calling my wrapper in the xml file, I don't have to specify the full path but then from my wrapper if I want to call my main script I can't if this one is not on the PATH ? the wrapper current directory is the job_working_directory, there is anyway to access my main script just like it's done for the wrapper ? thanks for your answer, Jerome Peter Cock a écrit :
On Mon, Jun 6, 2011 at 2:45 PM, Mariette <jmariett@toulouse.inra.fr> wrote:
Hi everyone,
I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ?
I use a wrapper script which moves the output file from the sub-directory to the location Galaxy requested.
Regarding the file format, if you only have one input file you can use format="input", otherwise use the change_format tag in the XML.
Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ?
An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ?
Normally the wrapper specifies the output format explicitly.
Peter ___________________________________________________________ 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:
On Tue, Jun 7, 2011 at 9:24 AM, Mariette <jmariett@toulouse.inra.fr> wrote:
Thanks for the answer,
so I tryed to write a wrapper, but the main script is not recognize. When I'm calling my wrapper in the xml file, I don't have to specify the full path but then from my wrapper if I want to call my main script I can't if this one is not on the PATH ? the wrapper current directory is the job_working_directory, there is anyway to access my main script just like it's done for the wrapper ?
Generally put the wrapper script next to your tool XML file, and don't prefix it with any path in the <command> tag in the XML, e.g. /opt/galaxy/tools/mariette/my_tool.xml /opt/galaxy/tools/mariette/my_tool.sh (or my_tool.py or my_tool.pl etc depending on what language you used) Your wrapper script then has to call the real executable, and the normal way to do this on Unix is to have it on the PATH. You could also hard code an absolute path. Peter
Thanks for the answer, Still considering the number of outputed files problem. In my script I know that if a cleaning option is set 2 other files will be created, so I check if the option is asked by the user and try this : <outputs> <data name="log" format="txt" /> #if $clean_pairends.clean_pairends_select=="y": <data name="output" format="input"/> #end if </outputs> but this is not working ... there is a way to do what I want ? thx Jerome Peter Cock a écrit :
On Tue, Jun 7, 2011 at 9:24 AM, Mariette <jmariett@toulouse.inra.fr> wrote:
Thanks for the answer,
so I tryed to write a wrapper, but the main script is not recognize. When I'm calling my wrapper in the xml file, I don't have to specify the full path but then from my wrapper if I want to call my main script I can't if this one is not on the PATH ? the wrapper current directory is the job_working_directory, there is anyway to access my main script just like it's done for the wrapper ?
Generally put the wrapper script next to your tool XML file, and don't prefix it with any path in the <command> tag in the XML, e.g.
/opt/galaxy/tools/mariette/my_tool.xml /opt/galaxy/tools/mariette/my_tool.sh
(or my_tool.py or my_tool.pl etc depending on what language you used)
Your wrapper script then has to call the real executable, and the normal way to do this on Unix is to have it on the PATH. You could also hard code an absolute path.
Peter ___________________________________________________________ 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:
On Tue, Jun 7, 2011 at 10:56 AM, Mariette <jmariett@toulouse.inra.fr> wrote:
Thanks for the answer, Still considering the number of outputed files problem. In my script I know that if a cleaning option is set 2 other files will be created, so I check if the option is asked by the user and try this :
<outputs> <data name="log" format="txt" /> #if $clean_pairends.clean_pairends_select=="y": <data name="output" format="input"/> #end if </outputs>
but this is not working ... there is a way to do what I want ? thx Jerome
The #if stuff is Cheetah syntax, and only applies within the <command> tag - not to the XML file in general. You probably want a conditional output using <when>, see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Peter
I can only see the usage of the <when> tag into the <outputs> to change format, is that correct ? I tryed : <outputs> <data name="log" format="txt" /> <data name="output" format="input"> <when input="clean_pairends.clean_pairends_select" value="y" format="interval"/> </data> </outputs> but even if the option is not selected, I have 2 outputs ! Am I missing something with the <when> tag ? Because it looks to me that it is pretty limited to the change_format tag, isn't it ? thx for your answers, Jerome Peter Cock a écrit :
On Tue, Jun 7, 2011 at 10:56 AM, Mariette <jmariett@toulouse.inra.fr> wrote:
Thanks for the answer, Still considering the number of outputed files problem. In my script I know that if a cleaning option is set 2 other files will be created, so I check if the option is asked by the user and try this :
<outputs> <data name="log" format="txt" /> #if $clean_pairends.clean_pairends_select=="y": <data name="output" format="input"/> #end if </outputs>
but this is not working ... there is a way to do what I want ? thx Jerome
The #if stuff is Cheetah syntax, and only applies within the <command> tag - not to the XML file in general.
You probably want a conditional output using <when>, see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Peter
___________________________________________________________ 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:
On Tue, Jun 7, 2011 at 11:38 AM, Mariette <jmariett@toulouse.inra.fr> wrote:
I can only see the usage of the <when> tag into the <outputs> to change format, is that correct ?
On re-reading the wiki page, yes, I think you are right. I should have said <filter> with <data>, as in tools/filters/sff_extractor.xml Peter
Thanks this is what I was looking for !! I succeded to make it work when checking the value on a simple param using the name like this <inputs> <param name="qual_file" type="data" format="qual" optional="true" label="Quality reads file (if input is a fasta)" /> </input> ... <outputs> <data name="out_qual" format="qual"> <filter>qual_file != None</filter> </data> </outputs> however when I'm in a conditional tag like this, I tryed : <inputs> <conditional name="clean_pairends"> <param name="clean_pairends_select" type="select" label="Clean pairends"> <option value="y">Yes</option> <option selected="true" value="n">No</option> </param> <when value="y"> <param name="border_limit" type="integer" size="10" value="70" label="Minimal length between the spacer and the read extremity"/> <param name="missmatch" type="integer" size="10" value="10" label="Limit of missmatch"/> </when> <when value="n"> </when> </conditional> </input> ... <outputs> <data name="out_pe_fasta" format="fasta"> <filter>clean_pairends.clean_pairends_select == "y"</filter> </data> but it's not working ... it looks like between filter tag I should provide a python test, am I missing something ? thx, Jerome Peter Cock a écrit :
On Tue, Jun 7, 2011 at 11:38 AM, Mariette <jmariett@toulouse.inra.fr> wrote:
I can only see the usage of the <when> tag into the <outputs> to change format, is that correct ?
On re-reading the wiki page, yes, I think you are right. I should have said <filter> with <data>, as in tools/filters/sff_extractor.xml
Peter ___________________________________________________________ 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:
So I tryed an other way to access the value : <data name="out_pe_fasta" format="fasta"> <filter>${clean_pairends.clean_pairends_select} == "y"</filter> </data> but it's not working either ... I tryed to add a label to the data like this : <data name="out_pe_fasta" format="fasta" label="${clean_pairends.clean_pairends_select}"> <filter>${clean_pairends.clean_pairends_select} == "y"</filter> </data> the data file is created with a label "n" ! Is it not weird ? Jerome Mariette a écrit :
Thanks this is what I was looking for !! I succeded to make it work when checking the value on a simple param using the name like this
<inputs> <param name="qual_file" type="data" format="qual" optional="true" label="Quality reads file (if input is a fasta)" /> </input> ... <outputs> <data name="out_qual" format="qual"> <filter>qual_file != None</filter> </data> </outputs>
however when I'm in a conditional tag like this, I tryed :
<inputs> <conditional name="clean_pairends"> <param name="clean_pairends_select" type="select" label="Clean pairends"> <option value="y">Yes</option> <option selected="true" value="n">No</option> </param> <when value="y"> <param name="border_limit" type="integer" size="10" value="70" label="Minimal length between the spacer and the read extremity"/> <param name="missmatch" type="integer" size="10" value="10" label="Limit of missmatch"/> </when> <when value="n"> </when> </conditional> </input> ... <outputs> <data name="out_pe_fasta" format="fasta"> <filter>clean_pairends.clean_pairends_select == "y"</filter> </data>
but it's not working ... it looks like between filter tag I should provide a python test, am I missing something ? thx, Jerome
Peter Cock a écrit :
On Tue, Jun 7, 2011 at 11:38 AM, Mariette <jmariett@toulouse.inra.fr> wrote:
I can only see the usage of the <when> tag into the <outputs> to change format, is that correct ?
On re-reading the wiki page, yes, I think you are right. I should have said <filter> with <data>, as in tools/filters/sff_extractor.xml
Peter ___________________________________________________________ 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:
___________________________________________________________ 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:
participants (2)
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Mariette -
Peter Cock