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