<commit_before><tool id="get_feature_info" name="Get features by Ensembl ID" version="0.1.2">
    <description>using REST API</description>
    <requirements>
        <requirement type="package" version="2.12.4">requests</requirement>
        <requirement type="package" version="1.10.0">six</requirement>
    </requirements>
    <command>
<![CDATA[
python $__tool_directory__/get_feature_info.py
-e $expand
-f $format_selector
-i "$input"
-s $species_selector
> "$output"
]]>
    </command>

    <inputs>
    <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" />
    <param name="species_selector" type="select" label="Select species">
        <option value="ensembl" selected="true">Vertebrates</option>
        <option value="ensemblgenomes">Other species</option>
    </param>
    <param name="expand" type="boolean" truevalue="1" falsevalue="0" label="Expand the search to include any connected features" help="For example, if the object is a gene, its transcripts, translations and exons will be returned as well" />
    <param name="format_selector" type="select" label="Output format">
        <option value="full" selected="true">Full</option>
        <option value="condensed">Condensed</option>
    </param>
    </inputs>

    <outputs>
        <data name="output" format="json" label="$(tool.name) on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="input" ftype="txt" value="input.txt" />
            <param name="expand" value="false" />
            <output name="outputFile" file="out.json" />
        </test>
    </tests>

    <help>
<![CDATA[
**What it does**

Retrieve feature information in JSON format from Ensembl using its REST API.

Uses the `"POST lookup/id"`_ API endpoint.

.. _"POST lookup/id": http://rest.ensembl.org/documentation/info/lookup_post
]]>
    </help>
    <citations>
    </citations>
</tool><commit_msg>Fix test output name<commit_after><tool id="get_feature_info" name="Get features by Ensembl ID" version="0.1.2">
    <description>using REST API</description>
    <requirements>
        <requirement type="package" version="2.12.4">requests</requirement>
        <requirement type="package" version="1.10.0">six</requirement>
    </requirements>
    <command>
<![CDATA[
python $__tool_directory__/get_feature_info.py
-e $expand
-f $format_selector
-i "$input"
-s $species_selector
> "$output"
]]>
    </command>

    <inputs>
    <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" />
    <param name="species_selector" type="select" label="Select species">
        <option value="ensembl" selected="true">Vertebrates</option>
        <option value="ensemblgenomes">Other species</option>
    </param>
    <param name="expand" type="boolean" truevalue="1" falsevalue="0" label="Expand the search to include any connected features" help="For example, if the object is a gene, its transcripts, translations and exons will be returned as well" />
    <param name="format_selector" type="select" label="Output format">
        <option value="full" selected="true">Full</option>
        <option value="condensed">Condensed</option>
    </param>
    </inputs>

    <outputs>
        <data name="output" format="json" label="$(tool.name) on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="input" ftype="txt" value="input.txt" />
            <param name="expand" value="false" />
            <output name="output" file="out.json" />
        </test>
    </tests>

    <help>
<![CDATA[
**What it does**

Retrieve feature information in JSON format from Ensembl using its REST API.

Uses the `"POST lookup/id"`_ API endpoint.

.. _"POST lookup/id": http://rest.ensembl.org/documentation/info/lookup_post
]]>
    </help>
    <citations>
    </citations>
</tool>
{'fraction_non_alphanumeric': 0.158482722785139, 'fraction_numerical': 0.00883346323720447, 'mean_word_length': 3.6497584541062804, 'pattern_counts': {'":': 2, '<': 91, '<?xml version=': 0, '>': 93, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2635976', 'n_tokens_mistral': 1218, 'n_tokens_neox': 1157, 'n_words': 306}