Mercurial > repos > devteam > cuffdiff
changeset 16:af3e173cad7f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
| author | iuc |
|---|---|
| date | Fri, 03 Jul 2020 11:43:55 -0400 |
| parents | 43b36b3d4333 |
| children | 43221aef70e2 |
| files | cuff_macros.xml cuffdiff_wrapper.xml |
| diffstat | 2 files changed, 198 insertions(+), 169 deletions(-) [+] |
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--- a/cuff_macros.xml Tue Jun 16 13:00:02 2020 -0400 +++ b/cuff_macros.xml Fri Jul 03 11:43:55 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/cuffdiff_wrapper.xml Tue Jun 16 13:00:02 2020 -0400 +++ b/cuffdiff_wrapper.xml Fri Jul 03 11:43:55 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.5"> +<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.6"> <description>find significant changes in transcript expression, splicing, and promoter use</description> <macros> <import>cuff_macros.xml</import> @@ -68,7 +68,7 @@ @CONDITION_SAMPLES@ #if $generate_sqlite: && - Rscript '$__tool_directory__/cummeRbund.R' && mv cummeRbund.sqlite '${output_cummerbund}' + Rscript '$__tool_directory__/cummeRbund.R' #end if ]]> </command> @@ -104,21 +104,21 @@ </param> <when value="Yes"> <conditional name="seq_source"> - <param name="index_source" type="select" label="Reference sequence data"> - <option value="cached">Locally cached</option> - <option value="history">History</option> - </param> - <when value="cached"> - <param name="index" type="select" label="Using reference genome"> - <options from_data_table="fasta_indexes"> - <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" /> - <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> - </options> + <param name="index_source" type="select" label="Reference sequence data"> + <option value="cached">Locally cached</option> + <option value="history">History</option> </param> - </when> - <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> - </when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> </conditional> </when> <when value="No"></when> @@ -209,36 +209,36 @@ </data> <!-- Standard datasets. --> <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" > - <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> + <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> </data> <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" > - <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> + <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> </data> <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff"> - <filter>not omit_tabular_output</filter> + <filter>not omit_tabular_output</filter> </data> <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking"> <filter>not omit_tabular_output</filter> @@ -256,72 +256,97 @@ <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking"> <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> </data> - <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database"> + <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" from_work_dir="cummeRbund.sqlite"> <filter>generate_sqlite</filter> </data> </outputs> <tests> <test> - <!-- - cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam - --> - <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> - <param name="generate_sqlite" value="yes" /> - <param name="omit_tabular_output" value="yes" /> - <conditional name="in_type"> - <param name="set_in_type" value="BAM" /> - <repeat name="conditions"> - <param name="name" value="q1" /> - <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> - </repeat> - <repeat name="conditions"> - <param name="name" value="q2" /> - <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> - </repeat> - </conditional> - <param name="fdr" value="0.05" /> - <param name="min_alignment_count" value="0" /> - <param name="do_bias_correction" value="No" /> - <param name="do_normalization" value="No" /> - <param name="multiread_correct" value="No"/> - <param name="sAdditional" value="No"/> - <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" /> + <!-- + cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam + --> + <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> + <param name="generate_sqlite" value="yes" /> + <param name="omit_tabular_output" value="yes" /> + <conditional name="in_type"> + <param name="set_in_type" value="BAM" /> + <repeat name="conditions"> + <param name="name" value="q1" /> + <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> + </repeat> + <repeat name="conditions"> + <param name="name" value="q2" /> + <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> + </repeat> + </conditional> + <param name="fdr" value="0.05" /> + <param name="min_alignment_count" value="0" /> + <param name="do_bias_correction" value="No" /> + <param name="do_normalization" value="No" /> + <param name="multiread_correct" value="No"/> + <param name="sAdditional" value="No"/> + <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" /> </test> <test> - <!-- - cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam - --> - <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> - <param name="omit_tabular_output" value="no" /> - <conditional name="in_type"> - <param name="set_in_type" value="BAM" /> - <repeat name="conditions"> - <param name="name" value="q1" /> - <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> - </repeat> - <repeat name="conditions"> - <param name="name" value="q2" /> - <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> - </repeat> - </conditional> - <param name="fdr" value="0.05" /> - <param name="min_alignment_count" value="0" /> - <param name="do_bias_correction" value="No" /> - <param name="do_normalization" value="No" /> - <param name="multiread_correct" value="No"/> - <param name="sAdditional" value="No"/> - <output name="splicing_diff" file="splicing.diff"/> - <output name="promoters_diff" file="promoters.diff"/> - <output name="cds_diff" file="cds.diff"/> - <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/> - <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/> - <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/> - <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/> - <output name="genes_exp" file="genes.exp" lines_diff="200"/> - <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/> - <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/> - <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/> + <!-- + Use a list collection as conditions input + cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam + --> + <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> + <param name="generate_sqlite" value="yes" /> + <param name="omit_tabular_output" value="yes" /> + <conditional name="in_type"> + <param name="set_in_type" value="CONDITION_LIST" /> + <param name="conditions"> + <collection type="list"> + <element name="q1" value="cuffdiff_in1.sam" /> + <element name="q2" value="cuffdiff_in2.sam" /> + </collection> + </param> + </conditional> + <param name="fdr" value="0.05" /> + <param name="min_alignment_count" value="0" /> + <param name="do_bias_correction" value="No" /> + <param name="do_normalization" value="No" /> + <param name="multiread_correct" value="No"/> + <param name="sAdditional" value="No"/> + <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" /> + </test> + <test> + <!-- + cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam + --> + <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> + <param name="omit_tabular_output" value="no" /> + <conditional name="in_type"> + <param name="set_in_type" value="BAM" /> + <repeat name="conditions"> + <param name="name" value="q1" /> + <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> + </repeat> + <repeat name="conditions"> + <param name="name" value="q2" /> + <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> + </repeat> + </conditional> + <param name="fdr" value="0.05" /> + <param name="min_alignment_count" value="0" /> + <param name="do_bias_correction" value="No" /> + <param name="do_normalization" value="No" /> + <param name="multiread_correct" value="No"/> + <param name="sAdditional" value="No"/> + <output name="splicing_diff" file="splicing.diff"/> + <output name="promoters_diff" file="promoters.diff"/> + <output name="cds_diff" file="cds.diff"/> + <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/> + <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/> + <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/> + <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/> + <output name="genes_exp" file="genes.exp" lines_diff="200"/> + <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/> + <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/> + <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/> </test> </tests> <help>