Mercurial > repos > devteam > cuffmerge
diff cuffmerge_wrapper.xml @ 10:b6e3849293b1 draft
Uploaded
author | devteam |
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date | Fri, 19 Dec 2014 11:59:06 -0500 |
parents | 424d49834830 |
children | 1707a530e598 |
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--- a/cuffmerge_wrapper.xml Mon Jan 20 11:09:02 2014 -0500 +++ b/cuffmerge_wrapper.xml Fri Dec 19 11:59:06 2014 -0500 @@ -1,12 +1,12 @@ -<tool id="cuffmerge" name="Cuffmerge" version="0.0.6"> - <!-- Wrapper supports Cuffmerge versions 1.3 and newer --> +<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0"> <description>merge together several Cufflinks assemblies</description> - <requirements> - <requirement type="package" version="2.1.1">cufflinks</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="stdio" /> + <macros> + <import>cuff_macros.xml</import> + </macros> <command interpreter="python"> cuffmerge_wrapper.py - --num-threads="\${GALAXY_SLOTS:-4}" ## Use annotation reference? @@ -16,29 +16,23 @@ ## Use sequence data? #if $seq_data.use_seq_data == "Yes": - -s + -s #if $seq_data.seq_source.index_source == "history": --ref_file="${seq_data.seq_source.ref_file}" #else: --index="${seq_data.seq_source.index.fields.path}" #end if #end if - + + --min-isoform-fraction="${min_isoform_fraction}" + ## Outputs. --merged-transcripts="${merged_transcripts}" - - ## Inputs. - "${first_input}" - #for $input_file in $input_files: - "${input_file.additional_input}" - #end for - + + @CUFFLINKS_GTF_INPUTS@ </command> <inputs> - <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> - <repeat name="input_files" title="Additional GTF Input Files"> - <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/> - </repeat> + <expand macro="cufflinks_gtf_inputs" /> <conditional name="annotation"> <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> <option value="No">No</option> @@ -65,7 +59,7 @@ <when value="cached"> <param name="index" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> - <filter type="data_meta" ref="first_input" key="dbkey" column="1" /> + <filter type="data_meta" ref="inputs" 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> @@ -76,6 +70,7 @@ </conditional> </when> </conditional> + <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" /> </inputs> <outputs> @@ -87,12 +82,12 @@ cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf --> <test> - <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/> - <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/> + <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> <param name="use_ref_annotation" value="Yes"/> <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> + <param name="min_isoform_fraction" value="0.08" /> <param name="use_seq_data" value="No"/> - <!-- oId assignment differ/are non-deterministic --> + <!-- oId assignment differ/are non-deterministic --> <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/> </test> </tests> @@ -102,8 +97,8 @@ Cuffmerge is part of Cufflinks_. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 -.. _Cufflinks: http://cufflinks.cbcb.umd.edu/ - +.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ + ------ **Know what you are doing** @@ -112,7 +107,7 @@ There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. -.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge +.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/ ------ @@ -130,5 +125,9 @@ Merged transcripts file: -Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> +Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. + </help> + <citations> + <citation type="doi">10.1038/nbt.1621</citation> + </citations> </tool>