annotate check_aln_design_file.xml @ 0:e979cb57a5d5 draft default tip

"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
author malex
date Thu, 14 Jan 2021 21:51:36 +0000
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1 <tool id="base_check_alignment_design_file" name="Check Alignment Design File" version="21.1.13">
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2 <description>for correct formatting and duplicate FASTQ names </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command><![CDATA[
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8 check_aln_design_file.py
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9 --design=$design
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10 --logfile=$logfile
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11 --dups=$dups
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12 ]]></command>
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13 <inputs>
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14 <param name="design" type="data" format="tabular,tsv" label="Alignment Design file" help="Design file containing FASTQ file names, sampleIDs, etc. Refer to the help section at the bottom of this page for the format. [Required]"/>
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="dups" label="${tool.name} on ${on_string}: FASTQ Duplicates"/>
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18 <data format="tabular" name="logfile" label="${tool.name} on ${on_string}: Alignment Design Criteria"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="design" ftype="data" value="align_and_counts_test_data/alignment_design_file.tsv"/>
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23 <output name="dups" ftype="data" file="align_and_counts_test_data/alignment_design_file_duplicates.tabular" />
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24 <output name="logfile" ftype="data" file="align_and_counts_test_data/alignment_design_file_criteria.csv" />
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25 </test>
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26 </tests>
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27 <help><![CDATA[
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28 **Tool Description**
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29
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30 This tool checks to make sure the Alignment design file is formatted correctly and has all needed headers. Also verifies that there are no duplicate FastQ file names.
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31 Default values are already in place to save user time.
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32
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33 **NOTE:** There are two Design Files that must be created and supplied by the user. They are the *Alignment Design File* and the *Comparate Design File*.
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34
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35 All others (Sample and Priors) are created and used as intermediates by the BASE workflows.
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36
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37 **The design file should contain the following columns, in order:**
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38
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39 (1) G1 - name of parental genome 1 for alignment
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40 (2) G2 - name of parental genome 2 for alignment
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41 (3) sampleID - sample identifier (no spaces)
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42 (4) fqName - name of the column containing the FASTQ file names, WITHOUT the extension
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43 (5) fqExtension - FASTQ file extension, for example, .fq or .fastq (NOT gzipped)
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44 (6) techRep - name of the column containing the technical replicates for each sampleID, for example, the same library run on different lanes.
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45 (7) readLength - the read length in base pairs
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46
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47 The sample identifier must contain the biological replicate number, and the comparate conditions to be tested in the Bayesian Model for Allelic Imbalance.
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48
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49 An example of a comparate condition is W1118_F, where W1118 is the genome and F refers to female. There must be at least two comparate conditions for Bayesian Analysis.
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50
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51 In the example below, there are two comparate condtions, W55_Mated and W55_Virgin, and E1 refers to the biological replicate number.
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52
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53 An example design file::
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54
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55 G1 G2 sampleID fqName fqExtension techRep readLength
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56 W1118 W55 mel_W55_Mated_E1 mel_W55_Mated_E1_R1 .fq 1 150
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57 W1118 W55 mel_W55_Mated_E1 mel_W55_Mated_E1_R2 .fq 2 150
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58 W1118 W55 mel_W55_Mated_E1 mel_W55_Mated_E1_R3 .fq 3 150
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59 W1118 W55 mel_W55_Virgin_E1 mel_W55_Virgin_E1_R1 .fq 1 150
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60 W1118 W55 mel_W55_Virgin_E1 mel_W55_Virgin_E1_R2 .fq 2 150
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61 W1118 W55 mel_W55_Virgin_E1 mel_W55_Virgin_E1_R3 .fq 3 150
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62
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63 If using simulated reads, include the technical replicate column, but label the technical replicates with the same number
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64
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65 Example design file for simulated data ::
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66
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67 G1 G2 sampleID fqName fqExtension techRep readLength
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68 W1118 W55 W55_M_1 SRR1989586_1 .fq 1 96
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69 W1118 W55 W55_M_2 SRR1989588_1 .fq 1 96
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70 W1118 W55 W55_V_1 SRR1989592_1 .fq 1 96
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71 W1118 W55 W55_V_2 SRR1989594_1 .fq 1 96
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72
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73 **Outputs**
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74
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75 (1) a logfile with information about whether the column names are correct and if there are any duplicated FASTQ file names.
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76 (2) a text file containing a list of any duplicated FASTQ file names, if present.
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77
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78 ]]></help>
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79 <citations>
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80 <citation type="bibtex">@ARTICLE{Miller20BASE,
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81 author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
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82 title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
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83 journal = {????},
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84 year = {submitted for publication}
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85 }</citation>
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86 </citations>
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87 </tool>