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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 |
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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> |