comparison lofreq_call.xml @ 3:3b4b2121842f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"

2:dfadc322b065

<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1">
    <description>with LoFreq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

                label="BED dataset with regions to examine" />
            </when>
        </conditional>
        <param name="variant_types" type="select"
        label="Types of variants to call"
        help="Note: When including indels in the called variants you should preprocess your input data to include indel alignment qualities">
            <option value="--call-indels">SNVs and indels</option>
            <option value="" selected="True">Only SNVs</option>
            <option value="--only-indels">Only indels</option>
        </param>
        <conditional name="call_control">
            <param name="set_call_options" type="select"
            label="Variant calling parameters">
                <option value="no">Use default settings</option>

            <conditional name="filter_control">
                <param name="filter_type" value="set_all_off" />
            </conditional>
            <output name="variants" file="call-out2.vcf" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[
lofreq call: call variants from BAM file
        
LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels

  For insertions/deletions this is defined, analogously, as the Phred-scaled
  likelihood that any inserted/deleted base is real, however, you are
  responsible for adding indel qualitites, which are required for indel
  calling with lofreq, to your input.

  For doing so, you can use ``lofreq indelqual`` or GATK's BQSR.

- Base/indel alignment quality

  For any read, this is the Phred-scaled likelihood that the read's base or
  indel mapped to a given reference genome position is mapped to this position

3:3b4b2121842f

<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2">
    <description>with LoFreq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

                label="BED dataset with regions to examine" />
            </when>
        </conditional>
        <param name="variant_types" type="select"
        label="Types of variants to call"
        help="Note: To have indels included in the called variants you HAVE to preprocess your input data using lofreq indelqual to include indel qualities. In addition, it is highly recommended that you calculate and make use of indel alignment qualities. See the detailed tool help below.">
            <option value="--call-indels">SNVs and indels</option>
            <option value="" selected="True">Only SNVs</option>
            <option value="--call-indels --only-indels">Only indels</option>
        </param>
        <conditional name="call_control">
            <param name="set_call_options" type="select"
            label="Variant calling parameters">
                <option value="no">Use default settings</option>

            <conditional name="filter_control">
                <param name="filter_type" value="set_all_off" />
            </conditional>
            <output name="variants" file="call-out2.vcf" lines_diff="4" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="indelqual-out3.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <param name="variant_types" value="--call-indels --only-indels" />
            <conditional name="filter_control">
                <param name="filter_type" value="set_all_off" />
            </conditional>
            <output name="variants" file="indel-call-out.vcf" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[
lofreq call: call variants from BAM file
        
LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels

  For insertions/deletions this is defined, analogously, as the Phred-scaled
  likelihood that any inserted/deleted base is real, however, you are
  responsible for adding indel qualitites, which are required for indel
  calling with lofreq, to your input.

  For doing so, you can use ``lofreq indelqual``.

- Base/indel alignment quality

  For any read, this is the Phred-scaled likelihood that the read's base or
  indel mapped to a given reference genome position is mapped to this position