comparison fastx_trimmer.xml @ 4:b98f3fa516a3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c

3:bbb007a39ac2

<tool id="cshl_fastx_trimmer" version="1.0.1" name="Trim sequences">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

@CATS@ fastx_trimmer -v
-f $first
-l $last
-o '$output'
@FQQUAL@
    ]]></command>
    <inputs>
        <expand macro="fastx_input" />
        <param name="first" type="integer" value="1" label="First base to keep" />
        <param name="last" type="integer" value="21" label="Last base to keep" />

            <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
            <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
            <param name="first" value="1"/>
            <param name="last" value="27"/>
            <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

4:b98f3fa516a3

<tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

@CATS@ fastx_trimmer -v
-f $first
-l $last
-o '$output'
@FQQUAL@

#if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
    -z
#end if

    ]]></command>
    <inputs>
        <expand macro="fastx_input" />
        <param name="first" type="integer" value="1" label="First base to keep" />
        <param name="last" type="integer" value="21" label="Last base to keep" />

            <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
            <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
            <param name="first" value="1"/>
            <param name="last" value="27"/>
            <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
        </test>
        <test>
            <!-- Trim a FASTQ.gz file  and output FASTQ.gz -->
            <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="first" value="1"/>
            <param name="last" value="27"/>
            <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**