Mercurial > repos > iuc > telescope_assign
diff telescope_assign.xml @ 0:66ff74923224 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
| author | iuc |
|---|---|
| date | Tue, 03 Sep 2019 18:12:09 -0400 |
| parents | |
| children | 2d8c943f3e8d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/telescope_assign.xml Tue Sep 03 18:12:09 2019 -0400 @@ -0,0 +1,173 @@ +<?xml version="1.0"?> +<tool id="telescope_assign" name="Reassign reads" version="@VERSION@"> + <description>with TELESCOPE using a statistical model</description> + <macros> + <token name="@VERSION@">1.0.3</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">telescope</requirement> + <requirement type="package" version="1.9">samtools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + mkdir tempdir && + mkdir outdir && + telescope assign '$input_alignment' '$input_gtf' + --tempdir tempdir + --outdir outdir + --ncpu \${GALAXY_SLOTS:-1} + $updated_sam + #if str($advanced.advanced_options) == 'select': + --reassign_mode $advanced.reassign_mode + --conf_prob $advanced.conf_prob + --overlap_mode $advanced.overlap_mode + --overlap_threshold $advanced.overlap_threshold + --annotation_class $advanced.annotation_class + --pi_prior $advanced.pi_prior + --theta_prior $advanced.theta_prior + --em_epsilon $advanced.em_epsilon + --max_iter $advanced.max_iter + $advanced.use_likelihood + #end if + #if $updated_sam + && + if [ -f outdir/telescope-updated.bam ] ; then + samtools sort outdir/telescope-updated.bam > '$updated_alignment' ; + else + echo 'Updated alignment file not found.' ; + exit 1 ; + fi + #end if + ]]></command> + <inputs> + <param name="input_alignment" type="data" format="sam,bam" label="Input SAM or BAM file" /> + <param name="input_gtf" type="data" format="gtf" label="Input annotation" /> + <param argument="--updated_sam" type="boolean" truevalue="--updated_sam" falsevalue="" label="Also output an updated BAM file with reassigned reads" /> + <conditional name="advanced"> + <param name="advanced_options" type="select" label="Advanced options"> + <option value="defaults">Use defaults</option> + <option value="select">Select values</option> + </param> + <when value="defaults" /> + <when value="select"> + <param argument="--reassign_mode" type="select" label="Reassignment mode" + help="After EM is complete, each fragment is reassigned according to the expected value of its membership weights. The reassignment method is the method for resolving the "best" reassignment for fragments that have multiple possible reassignments. Available modes are: "exclude" - fragments with multiple best assignments are excluded from the final counts; "choose" - the best assignment is randomly chosen from among the set of best assignments; "average" - the fragment is divided evenly among the best assignments; "conf" - only assignments that exceed a certain threshold (see --conf_prob) are accepted; "unique" - only uniquely aligned reads are included. NOTE: Results using all assignment modes are included in the Telescope report by default. This argument determines what mode will be used for the "final counts" column. (default: exclude)"> + <option value="exclude">Exclude</option> + <option value="choose">Choose</option> + <option value="average">Average</option> + <option value="conf">Conf</option> + <option value="unique">Unique</option> + </param> + <param argument="--conf_prob" type="float" value="0.9" min="0" max="1" label="Minimum probability for high confidence assignment" /> + <param argument="--overlap_mode" type="select" label="Overlap mode" help="The method used to determine whether a fragment overlaps feature"> + <option value="threshold">Threshold</option> + <option value="intersection-strict">Strict intersection</option> + <option value="union">Union</option> + </param> + <param argument="--overlap_threshold" type="float" value="0.2" min="0" max="1" label="Fraction of fragment that must be contained within a feature to be assigned to that locus" help="Ignored unless overlap mode is 'threshold'" /> + <param argument="--annotation_class" type="select" label="Annotation class" help="Both htseq and intervaltree appear to yield identical results. Performance differences are TBD."> + <option value="intervaltree">Interval tree</option> + <option value="htseq">HTSeq</option> + </param> + <param argument="--pi_prior" type="integer" value="0" label="Prior on π" help="Equivalent to adding n unique reads." /> + <param argument="--theta_prior" type="integer" value="0" label="Prior on θ" help="Equivalent to adding n non-unique reads." /> + <param argument="--em_epsilon" type="float" value="0.0000001" label="EM Algorithm υ cutoff" help="Default: 1e-7" /> + <param argument="--max_iter" type="integer" value="100" label="EM Algorithm maximum iterations" help="Default: 100" /> + <param argument="--use_likelihood" type="boolean" truevalue="--use_likelihood" falsevalue="" label="Use difference in log-likelihood as convergence criteria" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="outdir/telescope-telescope_report.tsv" /> + <data name="updated_alignment" format="bam"> + <filter>updated_sam</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_alignment" value="telescope-in1.bam" /> + <param name="input_gtf" value="telescope-in1.gtf" /> + <param name="updated_sam" value="true" /> + <output name="output" file="telescope-out1.tabular" /> + <output name="updated_alignment" file="telescope-out1.bam" /> + </test> + </tests> + <help><![CDATA[ +Output +------ + +Telescope has two main output files: the telescope report and an updated +SAM file (optional). The report file is most important for downstream +differential expression analysis since it contains the fragment count +estimates. The updated SAM file is useful for downstream locus-specific +analyses. + +Telescope report +~~~~~~~~~~~~~~~~ + +The first line in the telescope report is a comment (starting with a +“#”) that contains information about the run such as the number of +fragments processed, number of mapped fragments, number of uniquely and +ambiguously mapped fragments, and number of fragments mapping to the +annotation. The total number of mapped fragments may be useful for +normalization. + +The rest of the report is a table with calculated expression values for +individual transposable element locations. The columns of the table are: + +- ``transcript`` - Transcript ID, by default from "locus" field. See + --attribute argument to use a different attribute. +- ``transcript_length`` - Approximate length of transcript. This is + calculated from the annotation, not the data, and is equal to the + spanning length of the annotation minus any non-model regions. +- ``final_count`` - Total number of fragments assigned to transcript + after fitting the Telescope model. This is the column to use for + downstream analysis that models data as negative binomial, i.e. + DESeq2. +- ``final_conf`` - Final confident fragments. The number of fragments + assigned to transcript whose posterior probability exceeds a cutoff, + 0.9 by default. Set this using the --conf_prob argument. +- ``final_prop`` - Final proportion of fragments represented by + transcript. This is the final estimate of the π parameter. +- ``init_aligned`` - Initial number of fragments aligned to transcript. + A given fragment will contribute +1 to each transcript that it is + aligned to, thus the sum of this will be greater than the number of + fragments if there are multimapped reads. +- ``unique_count`` - Unique count. Number of fragments aligning + uniquely to this transcript. +- ``init_best`` - Initial number of fragments aligned to transcript + that have the "best" alignment score for that fragment. Fragments + that have the same best alignment score to multiple transcripts will + contribute +1 to each transcript. +- ``init_best_random`` - Initial number of fragments aligned to + transcript that have the "best" alignment score for that fragment. + Fragments that have the same best alignment score to multiple + transcripts will be randomly assigned to one transcript. + +Updated BAM file +~~~~~~~~~~~~~~~~ + +The updated BAM file contains those fragments that has at least 1 +initial alignment to a transposable element. The final assignment and +probabilities are encoded in the SAM tags: + +- ``ZF:Z`` Assigned Feature - The name of the feature that alignment is + assigned to. +- ``ZT:Z`` Telescope tag - A value of ``PRI`` indicates that this + alignment is the best hit for the feature and is used in the + likelihood calculations. Otherwise the value will be ``SEC``, meaning + that another alignment to the same feature has a higher score. +- ``ZB:Z`` Best Feature = The name(s) of the highest scoring feature(s) + for the fragment. +- ``YC:Z`` Specifies color for alignment as R,G,B. UCSC sanctioned tag, + see documentation `here.`_ +- ``XP:Z`` Alignment probability - estimated posterior probability for + this alignment. + +.. _here.: http://genome.ucsc.edu/goldenpath/help/hgBamTrackHelp.html + + ]]> + </help> + <citations> + <citation type="doi">10.1101/398172</citation> + </citations> +</tool> \ No newline at end of file