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planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
author rnateam
date Sat, 27 Oct 2018 13:11:24 -0400
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400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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1 <tool id="graphclust_aggregate_alignments" name="Aggregate and filter alignment metrics" version="0.1">
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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2 <description>of individual clusters, like the output of graphclust_align_cluster</description>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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3 <requirements>
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4 <requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
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5 <requirement type="package" version="0.23.0">pandas</requirement>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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6 </requirements>
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7 <command detect_errors="exit_code">
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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8 <![CDATA[
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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9 mkdir ./clusters_metrics &&
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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10 #import re
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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11 #for $tsv in $alignment_cons_tsv:
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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12 #set $safename_tsv = re.sub('[^\w\-_\.]', '_', $tsv.element_identifier)
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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13 ln -f -s '$tsv' ./clusters_metrics/${safename_tsv}.tsv &&
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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14 #end for
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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15 aggregate_align_metrics.py
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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16 --RNAz-prob-threshold $RNAz_prob_threshold
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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17 --rscape-bp-threshold $rscape_bp_threshold
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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18 --min-seq-num $min_seq_num
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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19 $exclude_spurious_structs
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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20 $additonal_columns
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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21 --clusters-tsv-pattern
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22 "clusters_metrics/*.tsv"
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23 --filtered-tsv-out filtered-alignment-metrics.tsv
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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24 --bed-out bed-cluster-locations.bed
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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25
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26 ]]></command>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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27 <inputs>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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28 <param type="data" name="alignment_cons_tsv" format="tabular" multiple="True" label="conservation-metrics-tsv"
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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29 help="Tabular tsv file of the computed conservation metrics from align cluster step"/>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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30 <param argument="min_seq_num" type="integer" value="3" label="Minimum cluster size"
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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31 help="Clusters with fewer seqeunces are excluded"/>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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32 <param argument="RNAz_prob_threshold" type="float" value="0.5" label="RNAz bed threshold"
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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33 help="Minimum RNAz SVM RNA-class probablity for bed annotation as RNAz hit"/>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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34 <param argument="rscape_bp_threshold" type="integer" value="2" label="Rscape bed threshold"
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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35 help="Minimum number of significant covarying basepairs by Rscape for bed annotation as Rscape hit"/>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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36 <param name="exclude_spurious_structs" type="boolean" checked="True" truevalue="--exclude-spurious-structs" falsevalue=""
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37 help="Exclude spurious alignment structs with poor SCI less than 0.01"/>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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38 <param name="additonal_columns" type="boolean" checked="False" truevalue="--all-columns" falsevalue="" help="Output additional prediction metrics"/>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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39 </inputs>
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40 <outputs>
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41 <data name="filtered_tsv" format="tabular" from_work_dir="filtered-alignment-metrics.tsv" label="filtered-alignment-metrics.tsv" />
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42 <data name="bed_clusters" format="tabular" from_work_dir="bed-cluster-locations.bed" label="bed-cluster-locations.bed" />
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="alignment_cons_tsv" value="1.alignment.cons.tsv,2.alignment.cons.tsv,3.alignment.cons.tsv"/>
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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47 <output name="filtered_tsv" file="metrics1.tsv" />
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48 <output name="bed_clusters" file="clusters1.bed" />
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 Aggregate and filter alignment metrics of individual clusters, like the output
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53 of graphclust_align_cluster
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54 ]]></help>
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55
400494a9274e planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
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56 <citations>
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57 <citation type="doi">10.5281/zenodo.597695</citation>
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58 </citations>
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59
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60 </tool>