Mercurial > repos > jjohnson > rmats
diff rmats.xml @ 0:ff15d6def09b draft
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/rmats commit 315f6ba609e9545c3a374f7fd471aee50b135ec8-dirty"
| author | jjohnson |
|---|---|
| date | Sat, 23 Jul 2022 21:23:48 +0000 |
| parents | |
| children | 74af9ab1a154 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmats.xml Sat Jul 23 21:23:48 2022 +0000 @@ -0,0 +1,269 @@ +<tool id="rmats" name="rMats turbo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> + <description>detect differential alternative splicing events from RNA-Seq</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + echo $b1 > b1.txt && + #if $b2 + echo $b2 > b2.txt && + #end if + rmats.py + --b1 b1.txt + #if $b2 + --b1 b1.txt + #end if + --gtf '$gtf' + #if $novel.novelSS == 'yes' + --novelSS + #if $novel.mil + --mil $novel.mil + #end if + #if $novel.mel + --mel $novel.mel + #end if + #end if + #if $readLength + --readLength $readLength + #end if + $variable_read_length + #if $libType + --libType "$libType" + #end if + #if $anchorLength + --anchorLength $anchorLength + #end if + #if $cstat + --cstat $cstat + #end if + $paired_stats + --nthread \${GALAXY_SLOTS:-1} + --tmp tmp + --od outputs + ]]></command> + <inputs> + <param name="b1" type="data" format="bam" multiple="true" label="BAM files for sample_1"/> + <param name="b2" type="data" format="bam" multiple="true" optional="true" label="BAM files for sample_2"/> + <param name="gtf" type="data" format="gtf" label="GTF - annotation of genes and transcripts"/> + + <conditional name="novel"> + <param name="novelSS" argument="--novelSS" type="select" label="Enable detection of novel splice sites"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="--mil" type="integer" value="" optional="true" label="Minimum Intron Length" help=" Default is 50"/> + <param argument="--mel" type="integer" value="" optional="true" label="Maximum Exon Length" help=" Default is 500"/> + </when> + </conditional> + <param argument="--readLength" type="integer" value="150" label="The length of each read"/> + <param name="variable_read_length" argument="--variable-read-length" type="boolean" truevalue="--variable-read-length" falsevalue="" checked="true" label="Allow reads with lengths that differ from --readLength to be processed"/> + + <param argument="--libType" type="select" optional="true" label="Library type" + help="Use fr-firststrand or fr-secondstrand for strand-specific data. Default: fr-unstranded"> + <option value="fr-unstranded">fr-unstranded</option> + <option value="fr-firststrand">fr-firststrand</option> + <option value="fr-secondstrand">fr-secondstrand</option> + </param> + + <param argument="--anchorLength" type="integer" value="" optional="true" label="The anchor length" help=" Default is 1"/> + + <param argument="--cstat" type="float" value="" min="0." max="1." optional="true" label="The cutoff splicing difference." help="The cutoff used in the null hypothesis test for differential splicing. The default is 0.0001 for 0.01% difference. Does not apply to the paired stats model"/> + <param name="paired_stats" argument="--paired-stats" type="boolean" truevalue="--paired-stats" falsevalue="" checked="true" label="Enable detection of novel splice sites"/> + + <param name="history_outputs" type="select" multiple="true" label="Select outputs"> + <option value="SE.MATS.JC.txt">SE.MATS.JC.txt</option> + <option value="SE.MATS.JCEC.txt">SE.MATS.JCEC.txt</option> + <option value="MXE.MATS.JC.txt">MXE.MATS.JC.txt</option> + <option value="MXE.MATS.JCEC.txt">MXE.MATS.JCEC.txt</option> + <option value="A3SS.MATS.JC.txt">A3SS.MATS.JC.txt</option> + <option value="A3SS.MATS.JCEC.txt">A3SS.MATS.JCEC.txt</option> + <option value="A5SS.MATS.JC.txt">A5SS.MATS.JC.txt</option> + <option value="A5SS.MATS.JCEC.txt">A5SS.MATS.JCEC.txt</option> + <option value="RI.MATS.JC.txt">RI.MATS.JC.txt</option> + <option value="RI.MATS.JCEC.txt">RI.MATS.JCEC.txt</option> + <option value="fromGTF.SE.txt">fromGTF.SE.txt</option> + <option value="fromGTF.novelJunction.SE.txt">fromGTF.novelJunction.SE.txt</option> + <option value="fromGTF.novelSpliceSite.SE.txt">fromGTF.novelSpliceSite.SE.txt</option> + <option value="fromGTF.MXE.txt">fromGTF.MXE.txt</option> + <option value="fromGTF.novelJunction.MXE.txt">fromGTF.novelJunction.MXE.txt</option> + <option value="fromGTF.novelSpliceSite.MXE.txt">fromGTF.novelSpliceSite.MXE.txt</option> + <option value="fromGTF.A3SS.txt">fromGTF.A3SS.txt</option> + <option value="fromGTF.novelJunction.A3SS.txt">fromGTF.novelJunction.A3SS.txt</option> + <option value="fromGTF.novelSpliceSite.A3SS.txt">fromGTF.novelSpliceSite.A3SS.txt</option> + <option value="fromGTF.A5SS.txt">fromGTF.A5SS.txt</option> + <option value="fromGTF.novelJunction.A5SS.txt">fromGTF.novelJunction.A5SS.txt</option> + <option value="fromGTF.novelSpliceSite.A5SS.txt">fromGTF.novelSpliceSite.A5SS.txt</option> + <option value="fromGTF.RI.txt">fromGTF.RI.txt</option> + <option value="fromGTF.novelJunction.RI.txt">fromGTF.novelJunction.RI.txt</option> + <option value="fromGTF.novelSpliceSite.RI.txt">fromGTF.novelSpliceSite.RI.txt</option> + </param> + + </inputs> + <outputs> + <data name="summary" format="tabular" label="${tool.name} on ${on_string}: summary.txt" from_work_dir="outputs/summary.txt"> + <expand macro="output_actions" column_names="@COLNAME_SUMMARY@"/> + </data> + + <data name="fromGTF_SE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.SE.txt" from_work_dir="outputs/fromGTF.SE.txt"> + <filter>history_outputs and 'fromGTF.SE.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_SE_GTF@"/> + </data> + <data name="fromGTF_A3SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.A3SS.txt" from_work_dir="outputs/fromGTF.A3SS.txt"> + <filter>history_outputs and 'fromGTF.A3SS.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/> + </data> + <data name="fromGTF_A5SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.A5SS.txt" from_work_dir="outputs/fromGTF.A5SS.txt"> + <filter>history_outputs and 'fromGTF.A5SS.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/> + </data> + <data name="fromGTF_MXE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.MXE.txt" from_work_dir="outputs/fromGTF.MXE.txt"> + <filter>history_outputs and 'fromGTF.MXE.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_MXE_GTF@"/> + </data> + <data name="fromGTF_RI" format="tabular" label="${tool.name} on ${on_string}: fromGTF.RI.txt" from_work_dir="outputs/fromGTF.RI.txt"> + <filter>history_outputs and 'fromGTF.RI.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_RI_GTF@"/> + </data> + + <data name="fromGTF_novelSpliceSite_SE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.SE.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.SE.txt"> + <filter>history_outputs and 'fromGTF.novelSpliceSite.SE.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_SE_GTF@"/> + </data> + <data name="fromGTF_novelSpliceSite_A3SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.A3SS.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.A3SS.txt"> + <filter>history_outputs and 'fromGTF.novelSpliceSite.A3SS.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/> + </data> + <data name="fromGTF_novelSpliceSite_A5SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.A5SS.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.A5SS.txt"> + <filter>history_outputs and 'fromGTF.novelSpliceSite.A5SS.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/> + </data> + <data name="fromGTF_novelSpliceSite_MXE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.MXE.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.MXE.txt"> + <filter>history_outputs and 'fromGTF.novelSpliceSite.MXE.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_MXE_GTF@"/> + </data> + <data name="fromGTF_novelSpliceSite_RI" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelSpliceSite.RI.txt" from_work_dir="outputs/fromGTF.novelSpliceSite.RI.txt"> + <filter>history_outputs and 'fromGTF.novelSpliceSite.RI.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_RI_GTF@"/> + </data> + + <data name="fromGTF_novelJunction_SE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.SE.txt" from_work_dir="outputs/fromGTF.novelJunction.SE.txt"> + <filter>history_outputs and 'fromGTF.novelJunction.SE.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_SE_GTF@"/> + </data> + <data name="fromGTF_novelJunction_A3SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.A3SS.txt" from_work_dir="outputs/fromGTF.novelJunction.A3SS.txt"> + <filter>history_outputs and 'fromGTF.novelJunction.A3SS.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/> + </data> + <data name="fromGTF_novelJunction_A5SS" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.A5SS.txt" from_work_dir="outputs/fromGTF.novelJunction.A5SS.txt"> + <filter>history_outputs and 'fromGTF.novelJunction.A5SS.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS_GTF@"/> + </data> + <data name="fromGTF_novelJunction_MXE" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.MXE.txt" from_work_dir="outputs/fromGTF.novelJunction.MXE.txt"> + <filter>history_outputs and 'fromGTF.novelJunction.MXE.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_MXE_GTF@"/> + </data> + <data name="fromGTF_novelJunction_RI" format="tabular" label="${tool.name} on ${on_string}: fromGTF.novelJunction.RI.txt" from_work_dir="outputs/fromGTF.novelJunction.RI.txt"> + <filter>history_outputs and 'fromGTF.novelJunction.RI.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_RI_GTF@"/> + </data> + + <data name="SE_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: SE.MATS.JCEC.txt" from_work_dir="outputs/SE.MATS.JCEC.txt"> + <filter>history_outputs and 'SE.MATS.JCEC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_SE@"/> + </data> + <data name="SE_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: SE.MATS.JC.txt" from_work_dir="outputs/SE.MATS.JC.txt"> + <filter>history_outputs and 'SE.MATS.JC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_SE@"/> + </data> + <data name="A3SS_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: A3SS.MATS.JCEC.txt" from_work_dir="outputs/A3SS.MATS.JCEC.txt"> + <filter>history_outputs and 'A3SS.MATS.JCEC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/> + </data> + <data name="A3SS_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: A3SS.MATS.JC.txt" from_work_dir="outputs/A3SS.MATS.JC.txt"> + <filter>history_outputs and 'A3SS.MATS.JC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/> + </data> + <data name="A5SS_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: A5SS.MATS.JCEC.txt" from_work_dir="outputs/A5SS.MATS.JCEC.txt"> + <filter>history_outputs and 'A5SS.MATS.JCEC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/> + </data> + <data name="A5SS_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: A5SS.MATS.JC.txt" from_work_dir="outputs/A5SS.MATS.JC.txt"> + <filter>history_outputs and 'A5SS.MATS.JC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_A_SS@"/> + </data> + <data name="MXE_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: MXE.MATS.JCEC.txt" from_work_dir="outputs/MXE.MATS.JCEC.txt"> + <filter>history_outputs and 'MXE.MATS.JCEC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_MXE@"/> + </data> + <data name="MXE_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: MXE.MATS.JC.txt" from_work_dir="outputs/MXE.MATS.JC.txt"> + <filter>history_outputs and 'MXE.MATS.JC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_MXE@"/> + </data> + <data name="RI_MATS_JCEC" format="tabular" label="${tool.name} on ${on_string}: RI.MATS.JCEC.txt" from_work_dir="outputs/RI.MATS.JCEC.txt"> + <filter>history_outputs and 'RI.MATS.JCEC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_RI@"/> + </data> + <data name="RI_MATS_JC" format="tabular" label="${tool.name} on ${on_string}: RI.MATS.JC.txt" from_work_dir="outputs/RI.MATS.JC.txt"> + <filter>history_outputs and 'RI.MATS.JC.txt' in history_outputs</filter> + <expand macro="output_actions" column_names="@COLNAMES_RI@"/> + </data> + </outputs> + <tests> + <test> + <param name="b1" ftype="bam" value="normal_small.bam"/> + <param name="b2" ftype="bam" value="cancer_small.bam"/> + <param name="gtf" ftype="gtf" value="GRCh38.gtf"/> + <param name="readLength" value="150"/> + <param name="variable_read_length" value="True"/> + <output name="summary" file="out/summary.txt" ftype="tabular"/> + </test> + + <test> + <param name="b1" ftype="bam" value="normal_small.bam"/> + <param name="b2" ftype="bam" value="cancer_small.bam"/> + <param name="gtf" ftype="gtf" value="GRCh38.gtf"/> + <param name="readLength" value="150"/> + <param name="variable_read_length" value="True"/> + <conditional name="novel"> + <param name="novelSS" value="yes"/> + <param name="mil" value="40"/> + </conditional> + <output name="summary" file="novel/summary.txt" ftype="tabular"/> + </test> + + <test> + <param name="b1" ftype="bam" value="normal_small.bam"/> + <param name="b2" ftype="bam" value="cancer_small.bam"/> + <param name="gtf" ftype="gtf" value="GRCh38.gtf"/> + <param name="readLength" value="150"/> + <param name="variable_read_length" value="True"/> + <conditional name="novel"> + <param name="novelSS" value="yes"/> + </conditional> + <param name="paired_stats" value="True"/> + <param name="" value="SE.MATS.JC.txt,MXE.MATS.JC.txt"/> + <output name="summary"> + <assert_contents> + <has_text_matching expression="EventType"/> + </assert_contents> + </output> + <output name="summary" file="novel/summary.txt" ftype="tabular"/> + </test> + + </tests> + <help><![CDATA[ +** rMATS ** + +RMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design. + +https://github.com/Xinglab/rmats-turbo#starting-with-bam-files + +https://github.com/Xinglab/rmats-turbo#output + + ]]></help> + <expand macro="citations" /> +</tool>