Mercurial > repos > iuc > cami_amber_add

annotate cami_amber_add_length.xml @ 5:320fef60c541 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 430cd92e7151f4ff87796589e7f51e4007aca38f
author iuc
date Mon, 10 Feb 2025 15:06:39 +0000
parents 22385c4e11a9
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22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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1 <tool id="cami_amber_add" name="CAMI AMBER add length column" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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2 <description>Create gold standard file for CAMI AMBER</description>
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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3 <macros>
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4 <import>macros.xml</import>
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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5 </macros>
5
320fef60c541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 430cd92e7151f4ff87796589e7f51e4007aca38f
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6 <expand macro="xrefs"/>
0
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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7 <expand macro="requirements" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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8 <command detect_errors="exit_code">
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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9 <![CDATA[
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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10
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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11 ln -s '${gold_standard_file}' '$gold_standard_file.element_identifier' &&
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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12 ln -s '${fasta_file}' '$fasta_file.element_identifier' &&
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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13
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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14 add_length_column.py
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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15 -g '$gold_standard_file.element_identifier'
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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16 -f '$fasta_file.element_identifier'
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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17 > gold_standard_file.tsv
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param argument="--gold_standard_file" type="data" format="tabular"
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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22 label="Input gold standard file here"
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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23 help="Input a binning file in biobox format to generate a biobox format file with the extra column 'Length' which is needed for AMBER. Every other biobox format can be used for this as well!" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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24 <param argument="--fasta_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz"
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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25 label="Input fasta/fastq file here"
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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26 help="Input the file which match to the gold standard file" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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27 </inputs>
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28 <outputs>
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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29 <data name="file" format="tabular" from_work_dir="gold_standard_file.tsv" label="${tool.name}: Gold standard file" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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30 </outputs>
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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31 <tests>
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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32 <test expect_num_outputs="1">
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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33 <param name="gold_standard_file" value="test_add.tsv" ftype="tabular" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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34 <param name="fasta_file" value="test_add.fasta.gz" ftype="fasta.gz" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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35 <output name="file" >
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36 <assert_contents>
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37 <has_size value="124000" delta="3000" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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38 </assert_contents>
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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39 </output>
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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40 </test>
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41 </tests>
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42 <help>
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43 <![CDATA[
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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44 .. class:: infomark
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45
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46 **What it does**
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47
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48 This tool can create the gold standard file which has to be used for the CAMI AMBER.
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49
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50 **Input**
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51
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52 This tool required 2 inputs:
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53
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54 - A binning file (biobox format)
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55
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56 This file can be created via the convert_to_biobox tool
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57
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58 .. class:: infomark
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59
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60 Example(tab separated):
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61
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62 ::
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63
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64 #CAMI Format for Binning
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65 @Version:0.9.0
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66 @SampleID:CAMI_low
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67 @@SEQUENCEID BINID
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68 RL|S1|C10 Bin_034
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69 RL|S1|C100 Bin_023
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70 RL|S1|C1000 Bin_034
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71 RL|S1|C10000 Bin_019
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72 RL|S1|C10002 Bin_035
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73 RL|S1|C10004 Bin_035
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74 RL|S1|C10008 Bin_034
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75 RL|S1|C10011 Bin_035
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76 RL|S1|C10012 Bin_013
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77 RL|S1|C10014 Bin_035
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78
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79 - A fasta/fastq file (fasta,fasta.gz,fastq,fastq.gz format)
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80
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81 This file need the identical sequences which are in the gold standard file to create the finish gold standard file for CAMI AMBER
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82
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83 **Output**
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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84
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85 As output the tool give you out a file in biobox format with the added column 'Length'. This file then can be used for AMBER as example!
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86
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87
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88 ]]>
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89 </help>
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90 <expand macro="citations" />
22385c4e11a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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91 </tool>