Mercurial > repos > rnateam > graphclust_aggregate_alignments
comparison graphclust_aggregate.xml @ 0:8778478a754f draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments commit 4406735e44aba20859c252be39f4e99df28c7a92
| author | rnateam |
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| date | Sat, 27 Oct 2018 13:20:46 -0400 |
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| -1:000000000000 | 0:8778478a754f |
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| 1 <tool id="graphclust_aggregate_alignments" name="Aggregate and filter alignment metrics" version="0.1"> | |
| 2 <description>of individual clusters, like the output of graphclust_align_cluster</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.6.0">graphclust-wrappers</requirement> | |
| 5 <requirement type="package" version="0.23.0">pandas</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 mkdir ./clusters_metrics && | |
| 10 #import re | |
| 11 #for $tsv in $alignment_cons_tsv: | |
| 12 #set $safename_tsv = re.sub('[^\w\-_\.]', '_', $tsv.element_identifier) | |
| 13 ln -f -s '$tsv' ./clusters_metrics/${safename_tsv}.tsv && | |
| 14 #end for | |
| 15 aggregate_align_metrics.py | |
| 16 --RNAz-prob-threshold $RNAz_prob_threshold | |
| 17 --rscape-bp-threshold $rscape_bp_threshold | |
| 18 --min-seq-num $min_seq_num | |
| 19 $exclude_spurious_structs | |
| 20 $additonal_columns | |
| 21 --clusters-tsv-pattern | |
| 22 "clusters_metrics/*.tsv" | |
| 23 --filtered-tsv-out filtered-alignment-metrics.tsv | |
| 24 --bed-out bed-cluster-locations.bed | |
| 25 | |
| 26 ]]></command> | |
| 27 <inputs> | |
| 28 <param type="data" name="alignment_cons_tsv" format="tabular" multiple="True" label="conservation-metrics-tsv" | |
| 29 help="Tabular tsv file of the computed conservation metrics from align cluster step"/> | |
| 30 <param argument="min_seq_num" type="integer" value="3" label="Minimum cluster size" | |
| 31 help="Clusters with fewer seqeunces are excluded"/> | |
| 32 <param argument="RNAz_prob_threshold" type="float" value="0.5" label="RNAz bed threshold" | |
| 33 help="Minimum RNAz SVM RNA-class probablity for bed annotation as RNAz hit"/> | |
| 34 <param argument="rscape_bp_threshold" type="integer" value="2" label="Rscape bed threshold" | |
| 35 help="Minimum number of significant covarying basepairs by Rscape for bed annotation as Rscape hit"/> | |
| 36 <param name="exclude_spurious_structs" type="boolean" checked="True" truevalue="--exclude-spurious-structs" falsevalue="" | |
| 37 help="Exclude spurious alignment structs with poor SCI less than 0.01"/> | |
| 38 <param name="additonal_columns" type="boolean" checked="False" truevalue="--all-columns" falsevalue="" help="Output additional prediction metrics"/> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data name="filtered_tsv" format="tabular" from_work_dir="filtered-alignment-metrics.tsv" label="filtered-alignment-metrics.tsv" /> | |
| 42 <data name="bed_clusters" format="tabular" from_work_dir="bed-cluster-locations.bed" label="bed-cluster-locations.bed" /> | |
| 43 </outputs> | |
| 44 <tests> | |
| 45 <test> | |
| 46 <param name="alignment_cons_tsv" value="1.alignment.cons.tsv,2.alignment.cons.tsv,3.alignment.cons.tsv"/> | |
| 47 <output name="filtered_tsv" file="metrics1.tsv" /> | |
| 48 <output name="bed_clusters" file="clusters1.bed" /> | |
| 49 </test> | |
| 50 </tests> | |
| 51 <help><![CDATA[ | |
| 52 Aggregate and filter alignment metrics of individual clusters, like the output | |
| 53 of graphclust_align_cluster | |
| 54 ]]></help> | |
| 55 | |
| 56 <citations> | |
| 57 <citation type="doi">10.5281/zenodo.597695</citation> | |
| 58 </citations> | |
| 59 | |
| 60 </tool> |