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"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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<tool id="check_sam_present" name="Verify that two input SAM files are present" version="21.1.13"> <description>verify 2 SAM files are present for every 1 FASTQ file.</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command><![CDATA[ check_sam_present.py --fq=$fq.element_identifier --alnType=$alnType --sam1=$sam1 --sam2=$sam2 --out=$out ]]></command> <inputs> <param name="alnType" size="30" type="select" value="" display="radio" label="Align Type" help="For BayesASE without modification, select Single End. Select whether SAM files were created from single end or paired end alignments."> <option value="SE" selected="true">Single End</option> <option value="PE" selected="true">Paired End</option> </param> <param name="sam1" type="data" format="sam" label="Unique SAM for G1" help="Select the SAM file [from BWASplitSAM] for updated genome1 containing only uniquely mapped reads."/> <param name="sam2" type="data" format="sam" label="Unique SAM for G2" help="Select the SAM file [from BWASplitSAM] for updated genome2 containing uniquely mapped reads. "/> <param name="fq" type="data" format="fastq" label="FastQ file" help="Select the FastQ file used to generate the SAM files." /> </inputs> <outputs> <data name="out" format="tabular" label="${tool.name} on ${on_string}:Check for 2 SAM Files"/> </outputs> <tests> <test> <param name="fq" ftype="data" value="align_and_counts_test_data/W55_M_1_1.fastq"/> <param name="alnType" ftype="select" value="SE"/> <param name="sam1" ftype="data" value="align_and_counts_test_data/W1118_G1_unique_sam_for_BASE.sam"/> <param name="sam2" ftype="data" value="align_and_counts_test_data/W55_G2_unique_sam_for_BASE.sam"/> <output name="out" file="align_and_counts_test_data/check_SAM_present_BASE_test_data.tabular" /> </test> </tests> <help><![CDATA[ **Tool Description** This tool checks to make sure that **2 SAM files** were generated from **1 FASTQ file** (one for each updated parental genome). **NOTE:** If you are running the BayesASE Align and Count workflow without modification, all reads are aligned as Single End - select Single End **Inputs** **FASTQ File [Required]** The FASTQ file used to generate the SAM files **Alignment Type [Required]** Select from drop-down menu how the FASTQ file was aligned - this will be SE if running the BayesASE workflow. **2 Unique SAM files [Required]** -Two SAM files containing uniquely mapping reads. These can be created by the *BWASplitSAM Tool*. (1) The unique SAM file generated by alignments to updated genome1 (2) The unique SAM file generated by alignments to updated genome2 **Output** (1) A single TSV file containing information on whether 2 SAM files are present per FASTQ file or not. Example of output: +-------------------+--------------------------+ | fqName | message | +===================+==========================+ |dataset_1795.dat | Have 2 SAM files - good! | +-------------------+--------------------------+ ]]></help> <citations> <citation type="bibtex">@ARTICLE{Miller20BASE, 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}, title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)}, journal = {????}, year = {submitted for publication} }</citation> </citations> </tool>