annotate create_sam_file_with_features.xml @ 0:e979cb57a5d5 draft default tip

"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"

<tool id="base_create_new_sam_file" name="Create new SAM file"  version="21.1.13">
    <description> with features of interest in RNAME field</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
        awk -v OFS='	' 'FNR==NR{a[$1,$2]=$7; next} {$3=a[$3,$4]}1' '$BED3' '$SAMFILE' | awk -F'\t'  '$3!=""' > '$NEWSAM'
]]>
    </command>
    <inputs>
        <param name="BED3" type="data" format="tabular" label="BED file generated from the Remove Reads That Do Not Overlap tool" />
        <param name="SAMFILE" type="data" format="sam" label="Input SAM file containing Uniquely Mapped Reads"
 help=" SAM file to convert chromosome names to feature IDs in RNAME field" />
    </inputs>
    <outputs>
        <data name="NEWSAM" format="sam" label="${tool.name} on ${on_string}: New SAM file with features instead of chrom" />
    </outputs>
    <tests>
        <test>
            <param name="BED3" value="align_and_counts_test_data/drop_nonintersecting_reads_for_BASE.tabular" ftype="tabular"/>
            <param name="SAMFILE" value="align_and_counts_test_data/W1118_G1_unique_sam_for_BASE.sam" ftype="sam"/>
            <output name="NEWSAM" file="align_and_counts_test_data/W1118_G1_create_new_SAM_file_with_features_BASE_test_data.sam" ftype="sam"/>
        </test>
    </tests>
    <help><![CDATA[
    **Tool Description**

This tool reformats the SAM file containing uniquely mapping reads using the multi-column BED file created by the *Remove reads that do not overlap with a feature for BASE* tool.
The resulting SAM file contains the name of genic features in the 'chrom' field.


----------------------------------------------------------------------------------------------

**Inputs**

    -The tool has two required inputs:

**BED File**
     The tool requires a BED file of reads overlapping genic features of interest.
     The *Remove reads that do not overlap with a feature for BayesASE* tool creates this BED file.

Example input BED file

    +---------------+---------+---------+---------+---------+------------+------------+
    |   Chrom       |  Start  |   End   |   Name  |  Score  | Strand     |ThickStart  |
    +===============+=========+=========+=========+=========+============+============+
    |      X        |  2190   |  2245   |   X     |    1    |    2300    |l(1)G0196   |
    +---------------+---------+---------+---------+---------+------------+------------+
    |      2R       |  1502   |  1834   |   2R    |     50  |19000       |Mapmodulin  |
    +---------------+---------+---------+---------+---------+------------+------------+

**Unique SAM File**
     Input the SAM file containing alignments for all uniquely mapping reads. This file can be created by the **BWASplitSAM** tool.

**Outputs**
     The tool outputs a new SAM file with the genic feature (ThickStart column in BED file) in the RNAME field instead of the chromosome name.

    ]]></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>