Many tools specify format="text" as data inputs or outputs

[mvdbeek]

This should be txt for the datatype, and might be confused with <param type="text"/> maybe ?

tools/stress_ng/stress_ng.xml:851:                <!--     <param argument="-\-job" type="data" format="text" -->
tools/EDeN/pyeden/predict.xml:20:        <data format="text" name="ofile_predictions" from_work_dir="predictions" label="${tool.name} on ${on_string}: Predictions"/>
tools/EDeN/pyeden/predict.xml:21:        <data format="text" name="ofile_margins" from_work_dir="margins" label="${tool.name} on ${on_string}: Margins"/>
tools/EDeN/pyeden/features.xml:20:        <data format="text" name="ofile_predictions" from_work_dir="features" label="${tool.name} on ${on_string}: Features"/>
tools/EDeN/pyeden/cluster_dbscan.xml:29:        <data format="text" name="ofile_vectorizer" from_work_dir="vectorizer" label="${tool.name} on ${on_string}: Vectorizer"/>
tools/EDeN/pyeden/cluster_dbscan.xml:30:        <data format="text" name="ofile_labels" from_work_dir="labels" label="${tool.name} on ${on_string}: Labels"/>
tools/EDeN/pyeden/nearest_neighbor.xml:31:        <data format="text" name="ofile_matrix" from_work_dir="matrix" label="${tool.name} on ${on_string}"/>
tools/EDeN/pyeden/cluster_kmeans.xml:28:        <data format="text" name="ofile_vectorizer" from_work_dir="vectorizer" label="${tool.name} on ${on_string}: Vectorizer"/>
tools/EDeN/pyeden/cluster_kmeans.xml:29:        <data format="text" name="ofile_labels" from_work_dir="labels" label="${tool.name} on ${on_string}: Labels"/>
tools/EDeN/pyeden/fit.xml:34:        <data format="text" name="ofile_vectorizer" from_work_dir="vectorizer" label="${tool.name} on ${on_string}: Vectorizer"/>
tools/EDeN/pyeden/fit.xml:35:        <data format="text" name="ofile_model" from_work_dir="model" label="${tool.name} on ${on_string}: Model"/>
tools/EDeN/pyeden/matrix.xml:49:        <data format="text" name="ofile_matrix" from_work_dir="matrix" label="${tool.name} on ${on_string}: Matrix"/>
tools/EDeN/pyeden/dendogram.xml:47:        <data format="text" name="ofile_linkage_matrix" from_work_dir="linkage_matrix" label="${tool.name} on ${on_string}: Linkage Matrix"/>
tools/gfastats/gfastats.xml:113:                    format="text" label="SAK input file" optional="true"
tools/gfastats/gfastats.xml:202:                <when input="tabular" value="false" format="text"/>
tools/sambamba/sambamba_depth.xml:69:        <data name="output" format="text"/>
tools/sambamba/Sambamba_view.xml:28:        <data name="output" format="text"/>
tools/openms/InspectAdapter.xml:199:    <param name="param_inspect_input" type="data" format="text" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/>
tools/openms/MascotAdapter.xml:130:    <param name="param_in" type="data" format="text" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
tools/openms/TICCalculator.xml:50:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/TopPerc.xml:163:    <param name="param_percolator_executable" type="data" format="text" label="Path to the percolator binary" help="(-percolator_executable) "/>
tools/openms/TopPerc.xml:183:    <param name="param_k" type="data" format="text" label="Input file given in the deprecated pin-xml format generated by" help="(-k) e.g. sqt2pin with the -k option"/>
tools/openms/TopPerc.xml:184:    <param name="param_W" type="data" format="text" label="Read initial weights to the given file" help="(-W) "/>
tools/openms/OpenSwathWorkflow.xml:362:      <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
tools/openms/MetaProSIP.xml:121:    <param name="param_r_executable" type="data" format="text" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
tools/openms/MzMLSplitter.xml:67:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/OpenSwathFileSplitter.xml:51:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/LabeledEval.xml:44:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/MapAlignmentEvaluation.xml:65:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/InternalCalibration.xml:100:    <param name="param_rscript_executable" type="data" format="text" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/>
tools/openms/XMLValidator.xml:36:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/SemanticValidator.xml:48:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/FuzzyDiff.xml:66:    <param name="param_in1" type="data" format="text" label="first input file" help="(-in1) "/>
tools/openms/FuzzyDiff.xml:67:    <param name="param_in2" type="data" format="text" label="second input file" help="(-in2) "/>
tools/openms/FuzzyDiff.xml:98:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/openms/DTAExtractor.xml:76:    <data name="param_stdout" format="text" label="Output from stdout"/>
tools/biopython/converters/sequence_converter.xml:59:        <data format="text" name="outfile" />
tools/genome_annotation_pipeline/eukaryotic_ncbi_submission.xml:82:        <param name="trainingset" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
tools/augustus/augustus.xml:94:        <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
tools/staging_area/blast_annotaion_from_genbank.xml:6:		<param name="input_genbank_file" type="data" format="text" label="Genbank File"/>
tools/staging_area/terpen_finder/terpen_finder.xml:20:        <param name="key_name" type="text" format="text" label="Compound Identifier encoded in the SDF-File." help="Specify the key name of the SDF metadata, that contains the molecule identifier."/>
tools/staging_area/terpen_finder/terpen_finder.xml:26:        <data name="output" format="text" />
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:147:	<param name="imageBackgroundColor" type="select" format="text">
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:165:		<param name="plot_type" type="select" format="text">
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:179:		<param name="plot_color" label='Color' type="select" format="text"  multiple='true'>
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:188:		<param name="plot_fill_color" label='Fill Color' type="select" format="text"  multiple='true'>
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:198:		<param name="plot_orientation" label='orientation' type="select" format="text">
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:208:		<param name="plot_axis_color" label='Color' type="select" format="text">
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:223:		<param name="plot_link_color" label='Link Color' type="select" format="text"  multiple='true'>
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:233:		<param name="plot_label_font" label='Label Font' type="select" format="text" >
tools/staging_area/circos/tools/circos/circosConfigFileCreatorWrapper.xml:252:			<param name="plot_rule_color" label='Rule Color' type="select" format="text" multiple='true'>
tools/staging_area/circos/tools/circos/circosWrapper.xml:148:	<param name="imageBackgroundColor" type="select" format="text" label='image background color' help='the image background color'>
tools/staging_area/circos/tools/circos/circosWrapper.xml:166:		<param name="plot_type" type="select" format="text">
tools/staging_area/circos/tools/circos/circosWrapper.xml:180:		<param name="plot_color" label='Color' type="select" format="text"  multiple='true' help='the plot color'>
tools/staging_area/circos/tools/circos/circosWrapper.xml:189:		<param name="plot_fill_color" label='Fill Color' type="select" format="text"  multiple='true' help='the plot fill color'>
tools/staging_area/circos/tools/circos/circosWrapper.xml:199:		<param name="plot_orientation" label='orientation' type="select" format="text">
tools/staging_area/circos/tools/circos/circosWrapper.xml:209:		<param name="plot_axis_color" label='Color' type="select" format="text" help='the plot axis color'>
tools/staging_area/circos/tools/circos/circosWrapper.xml:224:		<param name="plot_link_color" label='Link Color' type="select" format="text"  multiple='true' help='the plot link color'>
tools/staging_area/circos/tools/circos/circosWrapper.xml:234:		<param name="plot_label_font" label='Label Font' type="select" format="text" >
tools/staging_area/circos/tools/circos/circosWrapper.xml:253:			<param name="plot_rule_color" label='Rule Color' type="select" format="text" multiple='true' help='the rule color'>
tools/staging_area/ripcalWrapper.xml:15:	<param name='analysis_type' type="select" format="text" label='analysis type'>
tools/staging_area/ripcalWrapper.xml:21:	<param name='model' type="select" format="text" label='model'>
tools/rna_tools/infernal/cmalign.xml:177:        <data  name="outfile" format="text" label="cmalign on ${on_string}"/>
tools/rna_tools/rnaz/rnazRandomizeAln.xml:14:        <param type="data" name="input" format="text" />
tools/rna_tools/rnaz/rnazCluster.xml:16:        <param type="data" name="input" format="text" />
tools/rna_tools/locarna/locarna_multiple.xml:86:                <param name="input_data" type="data" format="text" label="Sequence input"
chemicaltoolbox/openbabel/ob_grep.xml:49:                <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
chemicaltoolbox/openbabel/change_title_to_metadata_value.xml:20:        <param name="key" type="text" format="text" label="Compound identifier encoded in the SD-file." help="Specify the key name of the SDF metadata which contains the molecule identifier (e.g. 'PUBCHEM_SHAPE_VOLUME')"/>
chemicaltoolbox/openbabel/ob_convert.xml:430:        <data name="outfile" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}">