comparison rename_scaffold.xml @ 6:2d143f0ac727 draft

planemo upload commit 921e3c4788a88874c4ac7b7097e609d0b1e646c9

5:7c8b327f298c

<tool id="rename_scaffold" name="rename the scaffolds" version="2.2">
    <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[
    python $__tool_directory__/rename.py $input $manipulate_selector $output $index

        <output name="output" file="fixed_reference_with_tab.fasta" />
        <output name="index" file="truncated_noascii_with_tab_name_mapping.csv"/>
    </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 '_' and also output a name mapping file.
]]></help>
<citations>
</citations>

6:2d143f0ac727

<tool id="rename_scaffold" name="rename the scaffolds" version="2.3">
    <description>a Galaxy tool to rename or truncate the scaffold names in the target genome so that they won't exceed 31 characters</description>
<stdio>
    <exit_code range="1:" />
</stdio>
<command><![CDATA[
    python $__tool_directory__/rename.py $input $manipulate_selector $output $index

        <output name="output" file="fixed_reference_with_tab.fasta" />
        <output name="index" file="truncated_noascii_with_tab_name_mapping.csv"/>
    </test>
</tests>
<help><![CDATA[
This tool is to rename scaffolds in the target 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 '_' and also output a name mapping file.
]]></help>
<citations>
</citations>