Mercurial > repos > malex > bayesase
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_sam_present.xml Thu Jan 14 21:51:36 2021 +0000 @@ -0,0 +1,83 @@ +<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>