Question: No case matched value Error with use of conditional statements
0
gravatar for bankapur
3.4 years ago by
bankapur0
United States
bankapur0 wrote:

Hi,

I am trying to integrate my own tool into galaxy on a local instance. My galaxy UI is designed such that when a user selects Tophat only then can he choose cufflinks and if cufflinks is true only then can a user select cufflinks annotation (a classic use case of <conditional> statement).

I get a "ValueError: ('No case matched value:', 'turn_on_cufflinks', [u'yestophat']) " error with the xml code I used. Will highly appreciate it if someone could make me understand why this error occurs and any ideas on how to correct it.

Here is a piece of xml file that I wrote to do the above mentioned:

<tool id="rnaseq_pipeline_test" name="rnaseq_pipeline">
<description>Running RNASEQ Pipeline</description>
<command>

#if str($sample_file) != "":
    make_config.py -s "$sample_file"
 #end if
#if str($genome_annotation) != "":
     -n "$genome_annotation"
 #end if
#if str($trimmomatic) == "yestrimmomatic":
    -t
#end if
#if str($tophat) == "yestophat":
    -o
 #end if
#if str($cufflinks) == "yescufflinks":
    -c
#end if
 #if str($cufflinksannotation) == "yescufflinksannotation":
    -a
#end if
#if str($rnaseqc) == "yesrnaseqc":
    -q
#end if
 #if str($rrnaquantitation) == "yesrrnaquantitation":
    -r
#end if
#if str($rsem) == "yesrsem":
    -m
#end if
#if $threads > 1:
    -e "$threads"
#end if
#if $max_process > 1:
    -j "$max_process"
#end if
 #if $output_directory:
     "$output_directory"
#end if
</command>
<inputs>
<param name= "sample_file" type="data" value="samples.txt" format="tabular" label="Sample File:"/>
<param name= "genome_annotation" type="select" label="Choose Genome Annotation:">
            <option value="/seq/regev_genome_portal/RESOURCES/candida/C_albicans_SC5314_version_A21-s02-m01-r01/Config/C_albicans_SC5314_extend100.config">C_albic    ans_SC5314_version_A21-s02-m01-r01[candida]</option>
</param>
<param name= "trimmomatic" type="select" label="Trimmomatic" display="checkboxes" multiple="true">
                   <option value="yestrimmomatic" selected="true">TRUE</option>
</param>
<conditional name="turn_on_cufflinks">
        <param name= "tophat" type="select" label="TopHat" display="checkboxes" multiple="true">
                    <option value="yestophat" selected="true">TRUE</option>
        </param>
            <when value = "yestophat">
                      <conditional name="turn_on_cufflinks_annotation">
                          <param name= "cufflinks" type="select" label="Cufflinks display="checkboxes" multiple="true">
                                <option value="yescufflinks"selected="true">TRUE</option>
                         </param>
                         <when value="yescufflinks">
                                 <param name= "cufflinksannotation" type="select" label="Cufflinks Annotation" display="checkboxes" multiple="true">
                                            <option value="yescufflinksannotation">TRUE</option>
                                </param>
                         </when>
         </conditional>
   </when>
</conditional>

 

Thank you 

Asma

conditional galaxy • 915 views
ADD COMMENTlink modified 3.4 years ago by Martin Čech ♦♦ 4.8k • written 3.4 years ago by bankapur0

I don't see a problem at a first look. I assume the error happens in the command line tag. It is probably best to show the complete xml file

 

Hans-Rudolf
 

ADD REPLYlink written 3.4 years ago by Hotz, Hans-Rudolf1.8k

I have edited my original post to include the entire xml file at this point. Let me know if you find error in the way the command line is constructed.

ADD REPLYlink written 3.4 years ago by bankapur0
0
gravatar for Hotz, Hans-Rudolf
3.4 years ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:
unless, this is a new feature I am not yet aware of, I would write

#if $turn_on_cufflinks.tophat == "yestophat":

 

instead of:

#if str($tophat) == "yestophat":

 

Hope this helps, Hans-Rudolf

 

ADD COMMENTlink written 3.4 years ago by Hotz, Hans-Rudolf1.8k
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