comparison macros.xml @ 6:28eb6a47be96 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

5:7b6dcfbdc6a9

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.2">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},
                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
            </citation>
            <citation type="doi">10.1093/bioinformatics/btp352</citation>
            <citation type="doi">10.1093/bioinformatics/btr076</citation>
            <citation type="doi">10.1093/bioinformatics/btr509</citation>
            <citation type="bibtex">

                url = {https://github.com/samtools/samtools},}
            </citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command>echo $(samtools --version | head -n 1)", "$(samtools --version | grep -o -E "htslib.*?")</version_command>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error" />
        </stdio>

3. Click **Datatype** tab
4. Set **New Type** to **BAM**
5. Click **Save**

The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.

    </token>

</macros>

6:28eb6a47be96

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.3.1">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.3.1</token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},
                url = {https://samtools.github.io/hts-specs/},}
            </citation>
            <citation type="doi">10.1093/bioinformatics/btp352</citation>
            <citation type="doi">10.1093/bioinformatics/btr076</citation>
            <citation type="doi">10.1093/bioinformatics/btr509</citation>
            <citation type="bibtex">

                url = {https://github.com/samtools/samtools},}
            </citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error" />
        </stdio>

3. Click **Datatype** tab
4. Set **New Type** to **BAM**
5. Click **Save**

The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
    </token>
</macros>