comparison delete_features.xml @ 10:df0e4eb2dfa5 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

9:2adc3aa47d15

    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <command detect_errors="aggressive"><![CDATA[
#if str($ask_one) == "yes":
	## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
	python $__tool_directory__/export.py
	@ADMIN_AUTH@
	@ORG_OR_GUESS@
	--gff "$gff_out"
	--fasta "$fasta_out"
	--json "$json_out"
    "$__user_email__"

    &&

	## Now we delete
	python $__tool_directory__/delete_features.py
	@ADMIN_AUTH@
	@ORG_OR_GUESS@
	"$__user_email__"
	#if str($filter) != "all"
		--type $filter
	#end if
	> $output;
#else
    echo "Nothing to do" > $output;
#end if
    ]]></command>
  <inputs>
    <expand macro="org_or_guess" />
    <param name="filter" type="select" label="Feature Type Filter">

        <option value="tRNA">tRNAs</option>
    </param>
    <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="Process and Error Log">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>

    <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
    <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
    <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
  </outputs>
  <tests>
      <test expect_failure="true">
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="Test org" />
          </conditional>
          <param name="filter" value="all"/>
          <param name="ask_one" value="yes"/>
          <expand macro="test_result" />
      </test>
  </tests>
  <help><![CDATA[
**What it does**

10:df0e4eb2dfa5

    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <command detect_errors="aggressive"><![CDATA[
@AUTH@

#if str($ask_one) == "yes":
	## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
	python '$__tool_directory__/export.py'
	@ORG_OR_GUESS@
	--gff '$gff_out'
        --fasta_pep '$fasta_pep'
        --fasta_cds '$fasta_cds'
        --fasta_cdna '$fasta_cdna'
        --vcf '$vcf_out'
	--json '$json_out'
  '$__user_email__'

    &&

	## Now we delete
	python '$__tool_directory__/delete_features.py'
	@ORG_OR_GUESS@
	'$__user_email__'
	#if str($filter) != "all"
		--type $filter
	#end if
	> '$output';
#else
    echo "Nothing to do" > '$output';
#end if
    ]]></command>
  <inputs>
    <expand macro="org_or_guess" />
    <param name="filter" type="select" label="Feature Type Filter">

        <option value="tRNA">tRNAs</option>
    </param>
    <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="Process and Error Log">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>

    <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
    <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
    <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
    <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
    <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
    <data format="json" name="json_out" label="Metadata from Apollo"/>
  </outputs>
  <tests>
      <test>
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="org4" />
          </conditional>
          <param name="filter" value="all"/>
          <param name="ask_one" value="yes"/>

          <output name="gff_out">
              <assert_contents>
                  <has_text text="##sequence-region Merlin 1 172788" />
                  <has_text text="owner=[e-mail];" />
                  <has_text text="Name=cds-not-under-exon" />
              </assert_contents>
          </output>
          <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
          <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
          <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
          <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
          <output name="json_out">
              <assert_contents>
                  <has_text text="org4" />
                  <has_text text="apollo_shared_dir/org4" />
              </assert_contents>
          </output>
          <output name="output">
              <assert_contents>
                  <has_text text="Deleted" />
                  <has_text text="[type=mRNA]" />
              </assert_contents>
          </output>
      </test>
  </tests>
  <help><![CDATA[
**What it does**