Mercurial > repos > devteam > cuffnorm
changeset 5:9a854107dbb2 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
| author | iuc |
|---|---|
| date | Fri, 03 Jul 2020 11:44:40 -0400 |
| parents | 6cbfede05833 |
| children | |
| files | cuff_macros.xml cuffnorm_wrapper.xml |
| diffstat | 2 files changed, 93 insertions(+), 95 deletions(-) [+] |
line wrap: on
line diff
--- a/cuff_macros.xml Tue Jun 16 13:01:30 2020 -0400 +++ b/cuff_macros.xml Fri Jul 03 11:44:40 2020 -0400 @@ -1,91 +1,95 @@ <macros> - <token name="@VERSION@">2.2.1</token> + <token name="@VERSION@">2.2.1</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.2.1">cufflinks</requirement> + <yield /> + </requirements> + </xml> - <xml name="requirements"> - <requirements> - <requirement type="package" version="2.2.1">cufflinks</requirement> - <yield /> - </requirements> - </xml> + <xml name="conditions_repeat" token_format=""> + <repeat name="conditions" title="Condition" min="2"> + <param name="name" label="Condition name" type="text"> + <validator type="empty_field" message="You must provide a condition name" /> + <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator> + </param> + <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/> + </repeat> + </xml> - <xml name="condition_inputs"> - <!-- DEFAULT : use BAM/SAM files --> - <conditional name="in_type"> - <param name="set_in_type" type="select" label="Input data type" - help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> - <option value="BAM">SAM/BAM</option> - <option value="CXB">Cuffquant (CXB)</option> - <option value="CONDITION_LIST">List of single replicate conditions</option> - <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> - </param> - <when value="BAM"> - <repeat name="conditions" title="Condition" min="2"> - <param name="name" label="Condition name" type="text"/> - <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> - </repeat> - </when> - <when value="CXB"> - <repeat name="conditions" title="Condition" min="2"> - <param name="name" label="Condition name" type="text"/> - <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> - </repeat> - </when> - <when value="CONDITION_LIST"> - <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> - </when> - <when value="CONDITION_REPLICATE_LIST"> - <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> - </when> - </conditional> - </xml> - <token name="@CONDITION_SAMPLES@"> - #if $in_type.set_in_type in ['BAM', 'CXB'] - #for $condition in $in_type.conditions: - #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) - '$samples' - #end for - #elif $in_type.set_in_type == 'CONDITION_LIST' - #for $sample in $in_type.conditions: - '$sample' - #end for - #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' - #for $condition_list in $in_type.conditions: - #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) - '$samples' - #end for - #end if - </token> - <token name="@CONDITION_LABELS@"> - #import re - #if $in_type.set_in_type in ['BAM', 'CXB'] - #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' - #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] - #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' - #end if - --labels $labels - </token> - <xml name="cufflinks_gtf_inputs"> - <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> - </xml> - <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[ - ## Inputs. - #for $i, $input_file in enumerate($inputs): - ln -s '${input_file}' input_$i && - #end for - ]]></token> - <token name="@CUFFLINKS_GTF_INPUTS@"> - ## Inputs. - #for $i, $input_file in enumerate($inputs): - 'input_$i' - #end for - </token> - <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> + <xml name="condition_inputs"> + <!-- DEFAULT : use BAM/SAM files --> + <conditional name="in_type"> + <param name="set_in_type" type="select" label="Input data type" + help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> + <option value="BAM">SAM/BAM</option> + <option value="CXB">Cuffquant (CXB)</option> + <option value="CONDITION_LIST">List of single replicate conditions</option> + <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> + </param> + <when value="BAM"> + <expand macro="conditions_repeat" format="sam,bam" /> + </when> + <when value="CXB"> + <expand macro="conditions_repeat" format="cxb" /> + </when> + <when value="CONDITION_LIST"> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> + </when> + <when value="CONDITION_REPLICATE_LIST"> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> + </when> + </conditional> + </xml> + <token name="@CONDITION_SAMPLES@"><![CDATA[ +#if $in_type.set_in_type in ['BAM', 'CXB'] + #for $condition in $in_type.conditions: + #set samples = ','.join([str($sample) for $sample in $condition.samples]) + '$samples' + #end for +#elif $in_type.set_in_type == 'CONDITION_LIST' + #for $sample in $in_type.conditions: + '$sample' + #end for +#elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' + #for $condition_list in $in_type.conditions: + #set samples = ','.join([str($sample) for $sample in $condition_list]) + '$samples' + #end for +#end if + ]]></token> + <token name="@CONDITION_LABELS@"><![CDATA[ +#import re +#if $in_type.set_in_type in ['BAM', 'CXB'] + #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions]) +#elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] + #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()]) +#end if +--labels '$labels' + ]]></token> + <xml name="cufflinks_gtf_inputs"> + <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> + </xml> + <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[ +## Inputs. +#for $i, $input_file in enumerate($inputs): + ln -s '${input_file}' input_$i && +#end for + ]]></token> + <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[ +## Inputs. +#for $i, $input_file in enumerate($inputs): + 'input_$i' +#end for + ]]></token> + <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> - <xml name="citations"> - <citations> - <citation type="doi">10.1038/nbt.1621</citation> - <yield/> - </citations> - </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.1621</citation> + <yield/> + </citations> + </xml> </macros>
--- a/cuffnorm_wrapper.xml Tue Jun 16 13:01:30 2020 -0400 +++ b/cuffnorm_wrapper.xml Fri Jul 03 11:44:40 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.2"> +<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.3"> <description>Create normalized expression levels</description> <macros> <import>cuff_macros.xml</import> @@ -210,7 +210,7 @@ **Input format** -Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. +Cuffnorm takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. ------ @@ -223,15 +223,9 @@ ------- -**Settings** - -All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. +**Parameter list** ------- - -**Cuffdiff parameter list** - -This is a list of implemented Cuffdiff options:: +This is a list of implemented Cuffnorm options:: --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags