Mercurial > repos > rnateam > graphclust_preprocessing

annotate preprocessing.xml @ 7:8634e06ae642 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust commit 4406735e44aba20859c252be39f4e99df28c7a92
author rnateam
date Sat, 27 Oct 2018 13:19:07 -0400
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1 <tool id="preproc" name="Preprocessing" version="0.5">
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2 <requirements>
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3 <requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
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4 <requirement type="package" version="3.0">zip</requirement>
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5 <requirement type="package" version="1.70">biopython</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command>
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12 <![CDATA[
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13 preprocessing.pl
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14 '$fastaFile'
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15 $max_length
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16 $in_winShift
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17 $min_seq_length
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19 #if $SHAPEdata:
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20 &&
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21 python '$__tool_directory__/splitSHAPE.py'
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22 '$SHAPEdata'
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5
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24 #end if
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26 #if $AlignmentData:
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27 &&
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28 python '$__tool_directory__/splitStockholm.py'
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29 '$AlignmentData'
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31 #end if
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0
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param type="data" name="fastaFile" format="fasta" />
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37 <param type="data" name="SHAPEdata" format="txt" optional="true" label="SHAPE data"/>
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38 <param type="data" name="AlignmentData" format="stockholm" optional="true" label="Alignments file"/>
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39 <param name="max_length" type="integer" value="10000" size="5" label="window size"/>
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40 <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/>
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41 <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/>
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42 </inputs>
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43 <outputs>
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44 <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/>
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45 <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/>
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46 <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/>
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47 <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/>
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48 <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/>
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49 <data name="shape_data_split" format="txt" from_work_dir="shape_data_split.react" label="SHAPE.data.split"/>
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50 <data name="alignment_data_split" format="stockholm" from_work_dir="alignment_data_split.stk" label="alignments.data.stk"/>
0
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="fastaFile" value="input.fa"/>
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55 <param name="max_length" value="10000"/>
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56 <param name="in_winShift" value="100"/>
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57 <param name="min_seq_length" value="5"/>
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58 <output name="data.fasta" file="FASTA/data.fasta"/>
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59 <output name="data.map" file="FASTA/data.map" />
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60 <output name="data.names" file="FASTA/data.names"/>
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61 <output name="data.fasta.scan" file="FASTA/data.fasta.scan" />
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62 </test>
0
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63
5
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64 <test>
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65 <param name="fastaFile" value="sample_3.fa"/>
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66 <param name="SHAPEdata" value="sample_3.react"/>
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67 <param name="max_length" value="100"/>
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68 <param name="in_winShift" value="50"/>
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69 <param name="min_seq_length" value="5"/>
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70 <output name="shape_data_split" file="sample_3_shape_data_split.react" />
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71 </test>
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72 <test>
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73 <param name="fastaFile" value="sample_4_representatives.fa"/>
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74 <param name="AlignmentData" value="sample_4_all.stk"/>
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75 <param name="max_length" value="50"/>
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76 <param name="in_winShift" value="50"/>
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77 <param name="min_seq_length" value="5"/>
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78 <output name="alignment_data_split" file="sample_4_alignment_data_split.stk" />
5
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79 </test>
f4ad5dceb619 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 9a3dc91fa984be18fabc0d968360634d787c9589
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80 </tests>
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a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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81 <help>
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82 <![CDATA[
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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83
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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84 **What it does**
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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85
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86 The tool takes as input a set of sequences in Fasta format and creates the final input for GraphCLust based on given parameters.
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87
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88 **Parameters**
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89
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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90 + **window size** : All input sequences are splitted into fragments of this length.
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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91 The shift of the sliding window can be defined via option *window shift in percent*.
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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92 This paramter reflects the expected length of signals to be found.
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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93 Slightly larger windows are usually ok. Too small windows can disturb existing signals.
a0f4b85dc739 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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94
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95
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96 + **window shift in percent** : Relative window size in % for window shift during input preprocessing.
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97 Please note that a small shift results in much more fragments for clustering. The benefit is that RNA
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98 motifs/structures are not destroyed by arbitrary split points. Smaller
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99 shifts usually increase the cluster quality. Too small shifts (<20) are not
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100 recommended as a dense center is "polluted" by overlapping fragments and
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101 no other occurences in the dataset can be found.
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102
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103
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104 + **minimum sequence length** : Minimal length of input sequences.
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105 Every input sequence below that length is ignored completely during clustering.
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106
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107 ]]></help>
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108 <citations>
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109 <citation type="doi">10.1093/bioinformatics/bts224</citation>
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110 </citations>
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111 </tool>