comparison rename_scaffold.xml @ 4:e35a3509c160 draft

planemo upload commit 3675b4447d11fb1cd75d505886e1bf693f9d07f5

3:9529a207d704

<tool id="rename_scaffold" name="rename the scaffolds" version="2.0">
    <description>a Galaxy tool to rename or truncate the scaffold names in the reference genome so that they won't exceed 31 characters</description>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[

    <test expect_failure="true">
        <!-- Test truncate input with non-ASCII charaters. Expect fail: name conflict! -->
        <param name="input" value="sequence_with_noascii_name_conflict.fa" />
        <param name="manipulate_selector" value="truncate" />
    </test>
</tests>
<help><![CDATA[
This tool is to rename scaffolds in the reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and also output a name mapping file.

Or truncate the scaffold names that are more than 31 characters and replace each non-ASCII character with '_'
]]></help>
<citations>
</citations>
</tool>

4:e35a3509c160

<tool id="rename_scaffold" name="rename the scaffolds" version="2.1">
    <description>a Galaxy tool to rename or truncate the scaffold names in the reference genome so that they won't exceed 31 characters</description>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[

    <test expect_failure="true">
        <!-- Test truncate input with non-ASCII charaters. Expect fail: name conflict! -->
        <param name="input" value="sequence_with_noascii_name_conflict.fa" />
        <param name="manipulate_selector" value="truncate" />
    </test>
    <test>
        <!-- Test input with tab -->
        <param name="input" value="sequence_with_tab.fa" />
        <param name="manipulate_selector" value="truncate" />
        <output name="output" file="fixed_reference_with_tab.fasta" />
    </test>
</tests>
<help><![CDATA[
This tool is to rename scaffolds in the reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and also output a name mapping file.

Or truncate the scaffold names that are more than 31 characters and replace each invalid character (non-ASCII, '\\t', '\\n', '\\x0b', '\\x0c', '\\r') with '_'
]]></help>
<citations>
</citations>
</tool>