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"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit b0be4c13808f3b2973aad4df5bfe87c6f41a3359"
author malex
date Thu, 14 Jan 2021 21:31:44 +0000
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8b2027117ce5 "planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit b0be4c13808f3b2973aad4df5bfe87c6f41a3359"
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1 <tool id="check_sam_present" name="Verify that two input SAM files are present" version="21.1.13">
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2 <description>verify 2 SAM files are present for every 1 FASTQ file.</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_sam_present.py
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9 --fq=$fq.element_identifier
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10 --alnType=$alnType
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11 --sam1=$sam1
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12 --sam2=$sam2
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13 --out=$out
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14 ]]></command>
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15 <inputs>
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16 <param name="alnType" size="30" type="select" value="" display="radio" label="Align Type" help="For BayesASE without modification, select Single End. Select whether SAM files were created from single end or paired end alignments.">
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17 <option value="SE" selected="true">Single End</option>
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18 <option value="PE" selected="true">Paired End</option>
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19 </param>
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20 <param name="sam1" type="data" format="sam" label="Unique SAM for G1" help="Select the SAM file [from BWASplitSAM] for updated genome1 containing only uniquely mapped reads."/>
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21 <param name="sam2" type="data" format="sam" label="Unique SAM for G2" help="Select the SAM file [from BWASplitSAM] for updated genome2 containing uniquely mapped reads. "/>
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22 <param name="fq" type="data" format="fastq" label="FastQ file" help="Select the FastQ file used to generate the SAM files." />
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23 </inputs>
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24 <outputs>
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25 <data name="out" format="tabular" label="${tool.name} on ${on_string}:Check for 2 SAM Files"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="fq" ftype="data" value="align_and_counts_test_data/W55_M_1_1.fastq"/>
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30 <param name="alnType" ftype="select" value="SE"/>
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31 <param name="sam1" ftype="data" value="align_and_counts_test_data/W1118_G1_unique_sam_for_BASE.sam"/>
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32 <param name="sam2" ftype="data" value="align_and_counts_test_data/W55_G2_unique_sam_for_BASE.sam"/>
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33 <output name="out" file="align_and_counts_test_data/check_SAM_present_BASE_test_data.tabular" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37
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38 **Tool Description**
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39
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40 This tool checks to make sure that **2 SAM files** were generated from **1 FASTQ file** (one for each updated parental genome).
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41
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42 **NOTE:** If you are running the BayesASE Align and Count workflow without modification, all reads are aligned as Single End - select Single End
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43
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44
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45 **Inputs**
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46
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47 **FASTQ File [Required]**
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48
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49 The FASTQ file used to generate the SAM files
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50
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51 **Alignment Type [Required]**
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52
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53 Select from drop-down menu how the FASTQ file was aligned - this will be SE if running the BayesASE workflow.
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54
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55 **2 Unique SAM files [Required]**
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56 -Two SAM files containing uniquely mapping reads. These can be created by the *BWASplitSAM Tool*.
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57
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58 (1) The unique SAM file generated by alignments to updated genome1
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59 (2) The unique SAM file generated by alignments to updated genome2
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60
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61
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62 **Output**
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63
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64 (1) A single TSV file containing information on whether 2 SAM files are present per FASTQ file or not.
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65
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66 Example of output:
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67
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68 +-------------------+--------------------------+
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69 | fqName | message |
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70 +===================+==========================+
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71 |dataset_1795.dat | Have 2 SAM files - good! |
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72 +-------------------+--------------------------+
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73
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74 ]]></help>
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75 <citations>
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76 <citation type="bibtex">@ARTICLE{Miller20BASE,
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77 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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78 title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
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79 journal = {????},
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80 year = {submitted for publication}
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81 }</citation>
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82 </citations>
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83 </tool>