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Replaced "query" with "dataset" in a number of tool definition XML files.

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I got tired of coming across "query" when doing workshops.
This commit is contained in:
Dave Clements
2013-01-14 16:13:54 -08:00
parent 3e1cdcf0fa
commit f706f34948
7 changed files with 12 additions and 12 deletions
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tools/extract/liftOver_wrapper.xml
+2 -2
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@@ -39,8 +39,8 @@
<param name="minChainT" type="hidden" value="0" />
</when>
<when value="1">
<param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/>
<param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/>
<param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/>
<param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/>
<param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
</when>
</conditional>
tools/filters/bed2gff.xml
+1 -1
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@@ -2,7 +2,7 @@
<description>converter</description>
<command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
<inputs>
<param format="bed" name="input" type="data" label="Convert this query"/>
<param format="bed" name="input" type="data" label="Convert this dataset"/>
</inputs>
<outputs>
<data format="gff" name="out_file1" />
tools/filters/condense_characters.xml
+1 -1
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@@ -12,7 +12,7 @@
<option value="U">Underscores</option>
<option value="P">Pipes</option>
</param>
<param format="txt" name="input" type="data" label="in this Query"/>
<param format="txt" name="input" type="data" label="in this Dataset"/>
</inputs>
<outputs>
<data format="input" name="out_file1" metadata_source="input" />
tools/filters/convert_characters.xml
+1 -1
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@@ -13,7 +13,7 @@
<option value="P">Pipes</option>
<option value="Co">Colons</option>
</param>
<param format="txt" name="input" type="data" label="in Query"/>
<param format="txt" name="input" type="data" label="in Dataset"/>
</inputs>
<outputs>
<data format="tabular" name="out_file1" />
tools/filters/gff2bed.xml
+1 -1
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@@ -2,7 +2,7 @@
<description>converter</description>
<command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
<inputs>
<param format="gff" name="input" type="data" label="Convert this query"/>
<param format="gff" name="input" type="data" label="Convert this dataset"/>
</inputs>
<outputs>
<data format="bed" name="out_file1" />
tools/filters/sorter.xml
+1 -1
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@@ -14,7 +14,7 @@
#end for
</command>
<inputs>
<param format="tabular" name="input" type="data" label="Sort Query" />
<param format="tabular" name="input" type="data" label="Sort Dataset" />
<param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/>
<param name="style" type="select" label="with flavor">
<option value="num">Numerical sort</option>
tools/new_operations/get_flanks.xml
+5 -5
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@@ -50,11 +50,11 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel
**Example 1**
- For the following query::
- For the following dataset::
chr22 1000 7000 NM_174568 0 +
- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**::
- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**::
chr22 500 800 NM_174568 0 +
@@ -62,11 +62,11 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel
**Example 2**
- For the following query::
- For the following dataset::
chr22 1000 7000 NM_028946 0 -
- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**::
- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::
chr22 500 800 NM_028946 0 -
@@ -75,4 +75,4 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel
</help>
</tool>
</tool>