comparison short_reads_trim_seq.xml @ 1:ece3c79e81ae draft default tip

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

0:8c0b907e6e5b

</command>
<inputs>
<page>
    <param name="input1" type="data" format="fasta" label="Reads" />
    <param name="input2" type="data" format="qualsolexa,qual454" label="Quality scores" />
	<param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
    <param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
    <conditional name="sequencing_method_choice">
        <param name="sequencer" type="select" label="Select technology">
            <option value="454">Roche (454) or ABI SOLiD</option>
            <option value="Solexa">Illumina (Solexa)</option>
        </param>

                <option value="yes">DO NOT trigger splitting </option>
                <option value="no">trigger splitting</option>
            </param>
        </when>
        <when value="Solexa">
            <param name="input3" type="integer" size="5" value="0" label="Restrict length of each read to" help="('0' = do not trim) The quality of Solexa reads drops towards the end. This option allows selecting the specified number of nucleotides from the beginning and then running the tool." />
        </when> 
    </conditional>
</page>
</inputs>

1:ece3c79e81ae

</command>
<inputs>
<page>
    <param name="input1" type="data" format="fasta" label="Reads" />
    <param name="input2" type="data" format="qualsolexa,qual454" label="Quality scores" />
	<param name="trim" type="integer" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
    <param name="length" type="integer" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
    <conditional name="sequencing_method_choice">
        <param name="sequencer" type="select" label="Select technology">
            <option value="454">Roche (454) or ABI SOLiD</option>
            <option value="Solexa">Illumina (Solexa)</option>
        </param>

                <option value="yes">DO NOT trigger splitting </option>
                <option value="no">trigger splitting</option>
            </param>
        </when>
        <when value="Solexa">
            <param name="input3" type="integer" value="0" label="Restrict length of each read to" help="('0' = do not trim) The quality of Solexa reads drops towards the end. This option allows selecting the specified number of nucleotides from the beginning and then running the tool." />
        </when> 
    </conditional>
</page>
</inputs>