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annotate sshmm.xml @ 0:f8a2a99a961d draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
author bgruening
date Fri, 06 Jul 2018 08:45:08 -0400
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0
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
bgruening
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1 <tool id="sshmm" name="ssHMM" version="1.0.7">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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2 <description>- RNA sequence-structure motif finder</description>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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3 <requirements>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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4 <requirement type="package" version="1.0.7">sshmm</requirement>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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5 </requirements>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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6 <command detect_errors="exit_code"><![CDATA[
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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7 python '$__tool_directory__/fasta_report_sequence_lengths.py' '$genome_fasta_file' > chrom.sizes &&
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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8 mkdir prepro_out &&
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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9 preprocess_dataset
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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10 prepro_out
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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11 prepro_id
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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12 '$input_bed_file'
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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13 '$genome_fasta_file'
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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14 chrom.sizes
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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15 #if $str_pred_method == 'rnashapes':
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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16 --disable_RNAstructure
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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17 #elif $str_pred_method == 'rnastructures':
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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18 --disable_RNAshapes
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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19 #end if
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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20 #if $advanced_prepro_params.advanced_prepro_params_selector == 'ap_specify':
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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21 $advanced_prepro_params.disable_filtering
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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22 --min_score $advanced_prepro_params.min_score
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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23 --min_length $advanced_prepro_params.min_length
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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24 --max_length $advanced_prepro_params.max_length
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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25 --elongation $advanced_prepro_params.elongation
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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26 #end if
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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27 &&
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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28 mkdir results
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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29 &&
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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30 train_seqstructhmm
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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31 prepro_out/fasta/prepro_id/positive.fasta
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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32 #if $str_pred_method == 'rnashapes':
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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33 prepro_out/shapes/prepro_id/positive.txt
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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34 #elif $str_pred_method == 'rnastructures':
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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35 prepro_out/structures/prepro_id/positive.txt
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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36 #end if
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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37 -o results
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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38 #if $advanced_train_params.advanced_train_params_selector == 'ap_specify':
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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39 --motif_length $advanced_train_params.motif_length
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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40 $advanced_train_params.init_random
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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41 --flexibility $advanced_train_params.flexibility
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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42 --block_size $advanced_train_params.block_size
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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43 --threshold $advanced_train_params.threshold
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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44 $advanced_train_params.only_best_shape
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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45 #end if
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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46 &&
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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47 mv results/job_* results/res_out
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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48 ]]></command>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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49 <inputs>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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50 <param name="input_bed_file" type="data" format="bed"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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51 label="Genomic binding sites BED file"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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52 help="Genomic BED file containing protein binding sites"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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53 <param name="genome_fasta_file" type="data" format="fasta"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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54 label="Genome reference FASTA file"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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55 help="Genomic FASTA file for extracting sequences defined in BED file"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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56 <param name="str_pred_method" type="select" label="Select structure prediction method">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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57 <option value="rnashapes" selected="true">RNAshapes</option>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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58 <option value="rnastructures">RNAstructures</option>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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59 </param>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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60 <conditional name="advanced_prepro_params">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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61 <param name="advanced_prepro_params_selector" type="select" label="Advanced preprocessing parameters">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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62 <option value="ap_not_specify" selected="true">Do not specify</option>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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63 <option value="ap_specify">Manually specify</option>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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64 </param>
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65 <when value="ap_not_specify" />
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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66 <when value="ap_specify">
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67 <param name="disable_filtering" truevalue="--disable_filtering" falsevalue="" checked="False"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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68 label="Skip the filtering step?" type="boolean"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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69 <param name="min_score" type="float" value="0.0"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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70 label="Filtering: minimum score for binding site" />
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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71 <param name="min_length" type="integer" value="8"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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72 label="Filtering: minimum binding site length" />
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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73 <param name="max_length" type="integer" value="75"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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74 label="Filtering: maximum binding site length" />
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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75 <param name="elongation" type="integer" value="20"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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76 label="Elongation: span for up- and downstream elongation of binding sites" />
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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77 </when>
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78 </conditional>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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79 <conditional name="advanced_train_params">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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80 <param name="advanced_train_params_selector" type="select" label="Advanced training parameters">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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81 <option value="ap_not_specify" selected="true">Do not specify</option>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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82 <option value="ap_specify">Manually specify</option>
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83 </param>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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84 <when value="ap_not_specify" />
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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85 <when value="ap_specify">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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86 <param name="motif_length" type="integer" value="6"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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87 label="Length of the motif that shall be found"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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88 <param name="init_random" truevalue="--random" falsevalue="" checked="False"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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89 label="Initialize the model randomly?" type="boolean"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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90 help="By default model is initialized with Baum-Welch optimized sequence motif"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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91 <param name="flexibility" type="integer" value="10"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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92 label="Greediness of Gibbs sampler"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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93 help="Model parameters are sampled from among the top f configurations (default: 10); set f to 0 in order to include all possible configurations"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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94 <param name="block_size" type="integer" value="1"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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95 label="Number of sequences to be held out in each iteration"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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96 <param name="threshold" type="integer" value="10"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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97 label="Termination threshold"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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98 help="The iterative algorithm is terminated if the given reduction in sequence structure log-likelihood is not reached for any of the 3 last measurements (default: 10)"/>
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99 <param name="only_best_shape" truevalue="--only-best-shape" falsevalue="" checked="False"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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100 label="Use only best structure for each sequence?" type="boolean"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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101 help="Train only using best structure for each sequence (default: use all structures)"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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102 </when>
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103 </conditional>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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104 <section name="output_options" title="Output options">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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105 <param name="output_prepro_files" type="boolean" value="False"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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106 help="Set to output FASTA file and corresponding structures file for the extracted genomic regions"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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107 label="Output FASTA file and corresponding structures file?"/>
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108 <param name="output_logo_files" type="boolean" value="False"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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109 help="Set to output logo_global.png, logo_hairpin.png, and logo_best_sequences.png files"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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110 label="Output logo files?"/>
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111 <param name="output_raw_files" type="boolean" value="False"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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112 help="Set to output final_model.xml, logo_best_sequences.txt, logo_global.txt, logo_hairpin.txt files"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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113 label="Output raw logo and model files?"/>
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114 </section>
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115 </inputs>
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116 <outputs>
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117 <data format="fasta" name="positive_fasta_out_file"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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118 label="${tool.name} on ${on_string} FASTA sequences (fasta)"
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119 from_work_dir="prepro_out/fasta/prepro_id/positive.fasta">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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120 <filter>
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121 output_options['output_prepro_files'] is True
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122 </filter>
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123 </data>
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124 <data format="txt" name="positive_rnashapes_out_file"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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125 label="${tool.name} on ${on_string} RNAshapes structures for sequences (txt)"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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126 from_work_dir="prepro_out/shapes/prepro_id/positive.txt">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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127 <filter>
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128 output_options['output_prepro_files'] is True and str_pred_method == 'rnashapes'
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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129 </filter>
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130 </data>
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131 <data format="txt" name="positive_rnastructures_out_file"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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132 label="${tool.name} on ${on_string} RNAstructures structures for sequences (txt)"
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133 from_work_dir="prepro_out/structures/prepro_id/positive.txt">
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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134 <filter>
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135 output_options['output_prepro_files'] is True and str_pred_method == 'rnastructures'
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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136 </filter>
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137 </data>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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138 <data format="png" name="final_graph_png"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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139 label="${tool.name} on ${on_string} final graph (png)"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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140 from_work_dir="results/res_out/final_graph.png"/>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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141 <data format="png" name="logo_best_sequences_png"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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142 label="${tool.name} on ${on_string} logo best sequences (png)"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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143 from_work_dir="results/res_out/logo_best_sequences.png">
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144 <filter>
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145 output_options['output_logo_files'] is True
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146 </filter>
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147 </data>
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148 <data format="png" name="logo_global_png"
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149 label="${tool.name} on ${on_string} logo global (png)"
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150 from_work_dir="results/res_out/logo_global.png">
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151 <filter>
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152 output_options['output_logo_files'] is True
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153 </filter>
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154 </data>
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155 <data format="png" name="logo_hairpin_png"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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156 label="${tool.name} on ${on_string} logo hairpin (png)"
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157 from_work_dir="results/res_out/logo_hairpin.png">
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158 <filter>
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159 output_options['output_logo_files'] is True
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160 </filter>
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161 </data>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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162 <data format="txt" name="logo_best_sequences_txt"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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163 label="${tool.name} on ${on_string} logo best sequences (txt)"
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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164 from_work_dir="results/res_out/logo_best_sequences.txt">
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165 <filter>
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166 output_options['output_raw_files'] is True
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167 </filter>
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168 </data>
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169 <data format="txt" name="logo_global_txt"
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170 label="${tool.name} on ${on_string} logo global (txt)"
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171 from_work_dir="results/res_out/logo_global.txt">
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172 <filter>
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173 output_options['output_raw_files'] is True
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174 </filter>
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175 </data>
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176 <data format="txt" name="logo_hairpin_txt"
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177 label="${tool.name} on ${on_string} logo hairpin (txt)"
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178 from_work_dir="results/res_out/logo_hairpin.txt">
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179 <filter>
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180 output_options['output_raw_files'] is True
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181 </filter>
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182 </data>
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183
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184 <data format="xml" name="final_model_xml"
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185 label="${tool.name} on ${on_string} final model (xml)"
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186 from_work_dir="results/res_out/final_model.xml">
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187 <filter>
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188 output_options['output_raw_files'] is True
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189 </filter>
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190 </data>
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191 </outputs>
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192 <tests>
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193 <test expect_num_outputs="10">
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194 <param name="input_bed_file" value="PUM2_sites_hsa_chrM.bed" ftype="bed"/>
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195 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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196 <param name="str_pred_method" value="rnastructures"/>
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197 <param name="advanced_prepro_params_selector" value="ap_specify"/>
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198 <param name="elongation" value="20"/>
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199 <param name="output_prepro_files" value="True"/>
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200 <param name="output_logo_files" value="True"/>
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201 <param name="output_raw_files" value="True"/>
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202 <output name="positive_fasta_out_file" file="hsa_chrM_positive.fasta" ftype="fasta"/>
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203 <output name="positive_rnastructures_out_file" file="hsa_chrM_structures_positive.txt" ftype="txt"/>
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204 <output name="final_graph_png" file="test_structure_final_graph.png" ftype="png" compare="sim_size" delta="40000"/>
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205 <output name="logo_global_png" file="test_structure_logo_global.png" ftype="png" compare="sim_size" delta="5000"/>
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206 <output name="logo_hairpin_png" file="test_structure_logo_hairpin.png" ftype="png" compare="sim_size" delta="5000"/>
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207 <output name="logo_best_sequences_png" file="test_structure_logo_best_sequences.png" ftype="png" compare="sim_size" delta="5000"/>
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208 <output name="logo_global_txt" file="test_structure_logo_global.txt" ftype="txt" compare="sim_size"/>
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209 <output name="logo_hairpin_txt" file="test_structure_logo_hairpin.txt" ftype="txt" compare="sim_size"/>
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210 <output name="logo_best_sequences_txt" file="test_structure_logo_best_sequences.txt" ftype="txt" compare="sim_size"/>
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211 <output name="final_model_xml" file="test_structure_final_model.xml" ftype="xml" compare="sim_size"/>
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212 </test>
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213 <test expect_num_outputs="10">
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214 <param name="input_bed_file" value="PUM2_sites_hsa_chrM.bed" ftype="bed"/>
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215 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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216 <param name="str_pred_method" value="rnashapes"/>
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217 <param name="output_prepro_files" value="True"/>
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218 <param name="output_logo_files" value="True"/>
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219 <param name="output_raw_files" value="True"/>
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220 <output name="positive_fasta_out_file" file="hsa_chrM_positive.fasta" ftype="fasta"/>
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221 <output name="positive_rnashapes_out_file" file="hsa_chrM_shapes_positive.txt" ftype="txt"/>
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222 <output name="final_graph_png" file="test_shapes_final_graph.png" ftype="png" compare="sim_size" delta="40000"/>
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223 <output name="logo_global_png" file="test_shapes_logo_global.png" ftype="png" compare="sim_size" delta="5000"/>
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224 <output name="logo_hairpin_png" file="test_shapes_logo_hairpin.png" ftype="png" compare="sim_size" delta="5000"/>
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225 <output name="logo_best_sequences_png" file="test_shapes_logo_best_sequences.png" ftype="png" compare="sim_size" delta="5000"/>
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226 <output name="logo_global_txt" file="test_shapes_logo_global.txt" ftype="txt" compare="sim_size"/>
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227 <output name="logo_hairpin_txt" file="test_shapes_logo_hairpin.txt" ftype="txt" compare="sim_size"/>
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228 <output name="logo_best_sequences_txt" file="test_shapes_logo_best_sequences.txt" ftype="txt" compare="sim_size"/>
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229 <output name="final_model_xml" file="test_shapes_final_model.xml" ftype="xml" compare="sim_size"/>
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230 </test>
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231 </tests>
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232 <help><![CDATA[
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233
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234 ssHMM is an RNA motif finder that recovers sequence-structure motifs from RNA-binding protein data, such as CLIP-Seq data. The tool input consists of a BED file with genomic binding regions and the corresponding genome reference FASTA file. For structure prediction, the user can select between RNAshapes and RNAstructures. Advanced parameters can be set for both the preprocessing and the training stage.
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235
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236 The output consists of a graph showing the found sequence motifs for the 5 structural contexts multiloop, hairpin, stem, internal loop, and exterior loop (output in .png format). The height of the nucleotides corresponds to their emission probabilities, while the thickness of the arrows corresponds to their transition probabilities. Additional files (intermediate, logo, model, raw) can be selected for output in the "Output options" section.
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237
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238 For more details have a look at the online documentation:
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239
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240 http://sshmm.readthedocs.io/en/latest/index.html
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241
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parents:
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242 ]]></help>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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parents:
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243 <citations>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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parents:
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244 <citation type="doi">10.1093/nar/gkx756</citation>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
bgruening
parents:
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245 </citations>
f8a2a99a961d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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246 </tool>